9RPV | pdb_00009rpv

Structure of the ZAK-bound human disome

  • Classification: RIBOSOME
  • Organism(s): Homo sapiens
  • Mutation(s): Yes 

  • Deposited: 2025-06-25 Released: 2025-12-10 
  • Deposition Author(s): Niu, S., Beckmann, R.
  • Funding Organization(s): European Research Council (ERC)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.35 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history. 


Literature

ZAK activation at the collided ribosome.

Huso, V.L., Niu, S., Catipovic, M.A., Saba, J.A., Denk, T., Park, E., Cheng, J., Berninghausen, O., Becker, T., Green, R., Beckmann, R.

(2025) Nature 

  • DOI: https://doi.org/10.1038/s41586-025-09772-8
  • Primary Citation of Related Structures:  
    9RPV, 9RSX

  • PubMed Abstract: 

    Ribosome collisions activate the ribotoxic stress response mediated by the MAP3K ZAK, which in turn regulates cell-fate consequences through downstream phosphorylation of the MAPKs p38 and JNK 1 . Despite the critical role of ZAK during cellular stress, a mechanistic and structural understanding of ZAK-ribosome interactions and how these lead to activation remain elusive. Here we combine biochemistry and cryo-electron microscopy to discover distinct ZAK-ribosome interactions required for constitutive recruitment and for activation. We find that upon induction of ribosome collisions, interactions between ZAK and the ribosomal protein RACK1 enable its activation by dimerization of its SAM domains at the collision interface. Furthermore, we discover how this process is negatively regulated by the ribosome-binding protein SERBP1 to prevent constitutive ZAK activation. Characterization of novel SAM variants as well as a known pathogenic variant of the SAM domain of ZAK supports a key role of the SAM domain in regulating kinase activity on and off the ribosome, with some mutants bypassing the ribosome requirement for ZAK activation. Collectively, our data provide a mechanistic blueprint of the kinase activity of ZAK at the collided ribosome interface.

    • Organizational Affiliation: 
    • Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA.

Macromolecules

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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Endothelial differentiation-related factor 1F [auth E4]148Homo sapiensMutation(s): 0 
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PHAROS:  O60869
GTEx:  ENSG00000107223 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L8K [auth LA]257Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000161016 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L3L [auth LB]403Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000100316 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L4FB [auth MC],
M [auth LC]		427Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000174444 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L5GB [auth MD],
N [auth LD]		297Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000122406 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL6HB [auth ME],
O [auth LE]		288Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000089009 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL30IB [auth MF],
P [auth LF]		248Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000147604 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L7aJB [auth MG],
Q [auth LG]		266Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000148303 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L9KB [auth MH],
R [auth LH]		192Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000163682 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein uL16-likeS [auth LI]214Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000165496 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L11MB [auth MJ],
T [auth LJ]		178Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000142676 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL13NB [auth ML],
U [auth LL]		211Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000167526 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L14OB [auth MM],
V [auth LM]		215Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000188846 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L15PB [auth MN],
W [auth LN]		204Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000174748 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L13aQB [auth MO],
X [auth LO]		203Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000142541 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L17RB [auth MP],
Y [auth LP]		184Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000265681 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L18SB [auth MQ],
Z [auth LQ]		188Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000063177 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L19AA [auth LR],
TB [auth MR]		196Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000108298 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L18aBA [auth LS],
UB [auth MS]		176Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000105640 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L21CA [auth LT],
VB [auth MT]		160Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000122026 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L22DA [auth LU],
WB [auth MU]		128Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000116251 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L23EA [auth LV],
XB [auth MV]		140Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000125691 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L24FA [auth LW],
YB [auth MW]		157Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000114391 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L23aGA [auth LX],
ZB [auth MX]		156Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000198242 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L26AC [auth MY],
HA [auth LY]		145Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000161970 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L27BC [auth MZ],
IA [auth LZ]		136Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000131469 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L27aJA [auth La]148Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000166441 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L29KA [auth Lb]159Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000162244 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L30EC [auth Mc],
LA [auth Lc]		115Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000156482 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L31FC [auth Md],
MA [auth Ld]		125Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000071082 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L32GC [auth Me],
NA [auth Le]		135Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000144713 
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L35aHC [auth Mf],
OA [auth Lf]		110Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000182899 
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L34IC [auth Mg],
PA [auth Lg]		117Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000109475 
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L35JC [auth Mh],
QA [auth Lh]		123Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000136942 
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L36KC [auth Mi],
RA [auth Li]		105Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000130255 
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL37LC [auth Mj],
SA [auth Lj]		97Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000145592 
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L38MC [auth Mk],
TA [auth Lk]		70Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000172809 
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L39NC [auth Ml],
UA [auth Ll]		51Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000198918 
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquitin-60S ribosomal protein L40VA [auth Lm]128Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000221983 
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L41PC [auth Mn],
WA [auth Ln]		25Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000229117 
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L36aXA [auth Lo]106Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000241343 
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L37aRC [auth Mp],
YA [auth Lp]		92Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000197756 
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L28ZA [auth Lr]137Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000108107 
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Entity ID: 55
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL2DB [auth MA]257Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000161016 
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Entity ID: 56
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL3EB [auth MB]403Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000100316 
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Entity ID: 57
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L10LB [auth MI]214Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000147403 
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Entity ID: 58
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL15CC [auth Ma]148Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000166441 
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Entity ID: 59
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL29DC [auth Mb]159Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000162244 
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Entity ID: 60
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquitin-ribosomal protein eL40 fusion proteinOC [auth Mm]128Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000221983 
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Entity ID: 61
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL42QC [auth Mo]106Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000241343 
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Entity ID: 62
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL28SC [auth Mr]137Homo sapiensMutation(s): 1 
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GTEx:  ENSG00000108107 
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Entity ID: 63
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L10aTC [auth Ms]217Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000198755 
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Entity ID: 64
MoleculeChains Sequence LengthOrganismDetailsImage
Mitogen-activated protein kinase kinase kinase 20UC [auth N1],
VC [auth N2]		800Homo sapiensMutation(s): 0 
EC: 2.7.11.25
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GTEx:  ENSG00000091436 
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Entity ID: 65
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS2WC [auth RA]295Homo sapiensMutation(s): 1 
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GTEx:  ENSG00000168028 
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Entity ID: 66
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S3aGE [auth SB],
XC [auth RB]		264Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000145425 
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Entity ID: 67
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S2HE [auth SC],
YC [auth RC]		293Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000140988 
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Entity ID: 68
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S3IE [auth SD],
ZC [auth RD]		243Homo sapiensMutation(s): 0 
EC: 4.2.99.18
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GTEx:  ENSG00000149273 
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Entity ID: 69
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein eS4, X isoformAD [auth RE],
JE [auth SE]		263Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000198034 
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Entity ID: 70
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S5BD [auth RF],
KE [auth SF]		204Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000083845 
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Entity ID: 71
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S6CD [auth RG],
LE [auth SG]		249Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000137154 
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Entity ID: 72
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S7DD [auth RH],
ME [auth SH]		194Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000171863 
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Entity ID: 73
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S8ED [auth RI],
NE [auth SI]		208Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000142937 
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Entity ID: 74
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S9FD [auth RJ],
OE [auth SJ]		194Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000170889 
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Entity ID: 75
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S10GD [auth RK],
PE [auth SK]		165Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000124614 
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Entity ID: 76
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S11HD [auth RL],
QE [auth SL]		158Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000142534 
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Entity ID: 77
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S12ID [auth RM],
JF [auth Sf]		132Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000112306 
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Entity ID: 78
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S13JD [auth RN],
RE [auth SN]		151Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000110700 
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Entity ID: 79
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S14KD [auth RO],
SE [auth SO]		151Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000164587 
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Entity ID: 80
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S15LD [auth RP],
TE [auth SP]		145Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000115268 
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Entity ID: 81
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S16MD [auth RQ],
UE [auth SQ]		146Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000105193 
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Entity ID: 82
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S17ND [auth RR],
VE [auth SR]		135Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000182774 
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Entity ID: 83
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S18OD [auth RS],
WE [auth SS]		152Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000231500 
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Entity ID: 84
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S19PD [auth RT],
XE [auth ST]		145Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000105372 
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Entity ID: 85
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S20QD [auth RU],
YE [auth SU]		119Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000008988 
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Entity ID: 86
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein eS21RD [auth RV]84Homo sapiensMutation(s): 1 
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GTEx:  ENSG00000171858 
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Entity ID: 87
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S15aAF [auth SW],
SD [auth RW]		130Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000134419 
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Entity ID: 88
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S23BF [auth SX],
TD [auth RX]		143Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000186468 
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Entity ID: 89
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S24CF [auth SY],
UD [auth RY]		133Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000138326 
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Entity ID: 90
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S25DF [auth SZ],
VD [auth RZ]		125Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000118181 
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Entity ID: 91
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S26EF [auth Sa],
WD [auth Ra]		115Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000197728 
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UniProt GroupP62854
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Entity ID: 92
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S27FF [auth Sb],
XD [auth Rb]		84Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000177954 
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Entity ID: 93
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S28GF [auth Sc],
YD [auth Rc]		69Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000233927 
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Entity ID: 94
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S29HF [auth Sd],
ZD [auth Rd]		56Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000213741 
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UniProt GroupP62273
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Entity ID: 95
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquitin-like FUBI-ribosomal protein eS30 fusion proteinAE [auth Re],
IF [auth Se]		133Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000149806 
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UniProt GroupP62861
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Entity ID: 96
MoleculeChains Sequence LengthOrganismDetailsImage
UbiquitinBE [auth Rf],
LF [auth sh]		156Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000143947 
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UniProt GroupP62979
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Entity ID: 97
MoleculeChains Sequence LengthOrganismDetailsImage
Receptor of activated protein C kinase 1CE [auth Rg],
KF [auth Sg]		317Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000204628 
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UniProt GroupP63244
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Entity ID: 100
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein SAFE [auth SA]295Homo sapiensMutation(s): 0 
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PHAROS:  P08865
GTEx:  ENSG00000168028 
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UniProt GroupP08865
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Entity ID: 101
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S21ZE [auth SV]83Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000171858 
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Entity ID: 1
MoleculeChains LengthOrganismImage
mRNA of the collided 80SA [auth A4]14Homo sapiens
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Entity ID: 2
MoleculeChains LengthOrganismImage
mRNA of the stalled 80SB [auth A5]8Homo sapiens
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Entity ID: 3
MoleculeChains LengthOrganismImage
P/E tRNA on the collided 80SC [auth B4]150Homo sapiens
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Entity ID: 4
MoleculeChains LengthOrganismImage
P-site tRNA of the stalled 80SD [auth B5]77Homo sapiens
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Entity ID: 5
MoleculeChains LengthOrganismImage
A/P tRNA on the collided 80SE [auth D4]152Homo sapiens
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Entity ID: 7
MoleculeChains LengthOrganismImage
E-site tRNA of the stalled 80SG [auth E5]75Homo sapiens
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Entity ID: 8
MoleculeChains LengthOrganismImage
28S rRNA of the collided 80SH [auth L5]5,070Homo sapiens
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Entity ID: 9
MoleculeChains LengthOrganismImage
5S rRNABB [auth M7],
I [auth L7]		120Homo sapiens
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Entity ID: 10
MoleculeChains LengthOrganismImage
5.8S rRNA of the collided 80SJ [auth L8]156Homo sapiens
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Entity ID: 53
MoleculeChains LengthOrganismImage
28S rRNA of the stalled 80SAB [auth M5]5,069Homo sapiens
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Entity ID: 54
MoleculeChains LengthOrganismImage
5.8S rRNA of the stalled 80SCB [auth M8]156Homo sapiens
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Entity ID: 98
MoleculeChains LengthOrganismImage
18S rRNA of the collided 80SDE [auth S2]1,869Homo sapiens
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Entity ID: 99
MoleculeChains LengthOrganismImage
18S rRNA of the stalled 80SEE [auth S3]1,869Homo sapiens
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Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ANM
Query on ANM
Download Ideal Coordinates CCD File 
JY [auth M5]ANISOMYCIN
C14 H19 N O4
YKJYKKNCCRKFSL-RDBSUJKOSA-N
ZN
Query on ZN
Download Ideal Coordinates CCD File 
NJ [auth Lg]
OJ [auth Lj]
QJ [auth Lm]
QLA [auth Sa]
RJ [auth Lo]
NJ [auth Lg],
OJ [auth Lj],
QJ [auth Lm],
QLA [auth Sa],
RJ [auth Lo],
RLA [auth Sd],
SJ [auth Lp]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG
Download Ideal Coordinates CCD File 
AAA [auth M5]
ABA [auth M5]
ACA [auth M8]
ADA [auth MP]
AEA [auth RN]
AAA [auth M5],
ABA [auth M5],
ACA [auth M8],
ADA [auth MP],
AEA [auth RN],
AFA [auth S2],
AG [auth L5],
AGA [auth S2],
AH [auth L5],
AHA [auth S3],
AI [auth L5],
AIA [auth S3],
AJ [auth L5],
AJA [auth S3],
AK [auth M5],
AKA [auth S3],
AL [auth M5],
ALA [auth S3],
AM [auth M5],
AN [auth M5],
AO [auth M5],
AP [auth M5],
AQ [auth M5],
AR [auth M5],
AS [auth M5],
AT [auth M5],
AU [auth M5],
AV [auth M5],
AW [auth M5],
AX [auth M5],
AY [auth M5],
AZ [auth M5],
BAA [auth M5],
BBA [auth M5],
BCA [auth M8],
BDA [auth MQ],
BEA [auth RO],
BFA [auth S2],
BG [auth L5],
BGA [auth S2],
BH [auth L5],
BHA [auth S3],
BI [auth L5],
BIA [auth S3],
BJ [auth L5],
BJA [auth S3],
BK [auth M5],
BKA [auth S3],
BL [auth M5],
BLA [auth S3],
BM [auth M5],
BN [auth M5],
BO [auth M5],
BP [auth M5],
BQ [auth M5],
BR [auth M5],
BS [auth M5],
BT [auth M5],
BU [auth M5],
BV [auth M5],
BW [auth M5],
BX [auth M5],
BY [auth M5],
BZ [auth M5],
CAA [auth M5],
CBA [auth M5],
CCA [auth M8],
CDA [auth MS],
CEA [auth RS],
CFA [auth S2],
CG [auth L5],
CGA [auth S2],
CH [auth L5],
CHA [auth S3],
CI [auth L5],
CIA [auth S3],
CJ [auth L5],
CJA [auth S3],
CK [auth M5],
CKA [auth S3],
CL [auth M5],
CLA [auth S3],
CM [auth M5],
CN [auth M5],
CO [auth M5],
CP [auth M5],
CQ [auth M5],
CR [auth M5],
CS [auth M5],
CT [auth M5],
CU [auth M5],
CV [auth M5],
CW [auth M5],
CX [auth M5],
CY [auth M5],
CZ [auth M5],
DAA [auth M5],
DBA [auth M5],
DCA [auth M8],
DDA [auth MS],
DEA [auth RT],
DFA [auth S2],
DG [auth L5],
DGA [auth S2],
DH [auth L5],
DHA [auth S3],
DI [auth L5],
DIA [auth S3],
DJ [auth L5],
DJA [auth S3],
DK [auth M5],
DKA [auth S3],
DL [auth M5],
DLA [auth S3],
DM [auth M5],
DN [auth M5],
DO [auth M5],
DP [auth M5],
DQ [auth M5],
DR [auth M5],
DS [auth M5],
DT [auth M5],
DU [auth M5],
DV [auth M5],
DW [auth M5],
DX [auth M5],
DY [auth M5],
DZ [auth M5],
EAA [auth M5],
EBA [auth M5],
ECA [auth M8],
EDA [auth MT],
EEA [auth RU],
EFA [auth S2],
EG [auth L5],
EGA [auth S2],
EH [auth L5],
EHA [auth S3],
EI [auth L5],
EIA [auth S3],
EJ [auth L7],
EJA [auth S3],
EK [auth M5],
EKA [auth S3],
EL [auth M5],
ELA [auth S3],
EM [auth M5],
EN [auth M5],
EO [auth M5],
EP [auth M5],
EQ [auth M5],
ER [auth M5],
ES [auth M5],
ET [auth M5],
EU [auth M5],
EV [auth M5],
EW [auth M5],
EX [auth M5],
EY [auth M5],
EZ [auth M5],
FAA [auth M5],
FBA [auth M5],
FCA [auth M8],
FDA [auth MV],
FEA [auth RX],
FFA [auth S2],
FG [auth L5],
FGA [auth S2],
FH [auth L5],
FHA [auth S3],
FI [auth L5],
FIA [auth S3],
FJ [auth L7],
FJA [auth S3],
FK [auth M5],
FKA [auth S3],
FL [auth M5],
FLA [auth S3],
FM [auth M5],
FN [auth M5],
FO [auth M5],
FP [auth M5],
FQ [auth M5],
FR [auth M5],
FS [auth M5],
FT [auth M5],
FU [auth M5],
FV [auth M5],
FW [auth M5],
FX [auth M5],
FY [auth M5],
FZ [auth M5],
GAA [auth M5],
GBA [auth M7],
GCA [auth M8],
GDA [auth MY],
GEA [auth Rd],
GFA [auth S2],
GG [auth L5],
GGA [auth S2],
GH [auth L5],
GHA [auth S3],
GI [auth L5],
GIA [auth S3],
GJ [auth L8],
GJA [auth S3],
GK [auth M5],
GKA [auth S3],
GL [auth M5],
GLA [auth S3],
GM [auth M5],
GN [auth M5],
GO [auth M5],
GP [auth M5],
GQ [auth M5],
GR [auth M5],
GS [auth M5],
GT [auth M5],
GU [auth M5],
GV [auth M5],
GW [auth M5],
GX [auth M5],
GY [auth M5],
GZ [auth M5],
HAA [auth M5],
HBA [auth M7],
HCA [auth M8],
HDA [auth Ma],
HEA [auth S2],
HFA [auth S2],
HG [auth L5],
HGA [auth S2],
HH [auth L5],
HHA [auth S3],
HI [auth L5],
HIA [auth S3],
HJ [auth L8],
HJA [auth S3],
HK [auth M5],
HKA [auth S3],
HL [auth M5],
HLA [auth S3],
HM [auth M5],
HN [auth M5],
HO [auth M5],
HP [auth M5],
HQ [auth M5],
HR [auth M5],
HS [auth M5],
HT [auth M5],
HU [auth M5],
HV [auth M5],
HW [auth M5],
HX [auth M5],
HY [auth M5],
HZ [auth M5],
IAA [auth M5],
IBA [auth M7],
ICA [auth MC],
IDA [auth Ma],
IEA [auth S2],
IFA [auth S2],
IG [auth L5],
IGA [auth S2],
IH [auth L5],
IHA [auth S3],
II [auth L5],
IIA [auth S3],
IJ [auth L8],
IJA [auth S3],
IK [auth M5],
IKA [auth S3],
IL [auth M5],
ILA [auth S3],
IM [auth M5],
IN [auth M5],
IO [auth M5],
IP [auth M5],
IQ [auth M5],
IR [auth M5],
IS [auth M5],
IT [auth M5],
IU [auth M5],
IV [auth M5],
IW [auth M5],
IX [auth M5],
IY [auth M5],
IZ [auth M5],
JAA [auth M5],
JBA [auth M7],
JCA [auth MD],
JDA [auth Mc],
JEA [auth S2],
JFA [auth S2],
JG [auth L5],
JGA [auth S2],
JH [auth L5],
JHA [auth S3],
JI [auth L5],
JIA [auth S3],
JJ [auth L8],
JJA [auth S3],
JK [auth M5],
JKA [auth S3],
JL [auth M5],
JLA [auth S3],
JM [auth M5],
JN [auth M5],
JO [auth M5],
JP [auth M5],
JQ [auth M5],
JR [auth M5],
JS [auth M5],
JT [auth M5],
JU [auth M5],
JV [auth M5],
JW [auth M5],
JX [auth M5],
JZ [auth M5],
KAA [auth M5],
KBA [auth M7],
KCA [auth MD],
KDA [auth Me],
KEA [auth S2],
KFA [auth S2],
KG [auth L5],
KGA [auth S2],
KH [auth L5],
KHA [auth S3],
KI [auth L5],
KIA [auth S3],
KJ [auth L8],
KJA [auth S3],
KK [auth M5],
KKA [auth S3],
KL [auth M5],
KLA [auth S3],
KM [auth M5],
KN [auth M5],
KO [auth M5],
KP [auth M5],
KQ [auth M5],
KR [auth M5],
KS [auth M5],
KT [auth M5],
KU [auth M5],
KV [auth M5],
KW [auth M5],
KX [auth M5],
KY [auth M5],
KZ [auth M5],
LAA [auth M5],
LBA [auth M7],
LCA [auth MF],
LDA [auth Mf],
LEA [auth S2],
LFA [auth S2],
LG [auth L5],
LGA [auth S2],
LH [auth L5],
LHA [auth S3],
LI [auth L5],
LIA [auth S3],
LJ [auth LQ],
LJA [auth S3],
LK [auth M5],
LKA [auth S3],
LL [auth M5],
LLA [auth S3],
LM [auth M5],
LN [auth M5],
LO [auth M5],
LP [auth M5],
LQ [auth M5],
LR [auth M5],
LS [auth M5],
LT [auth M5],
LU [auth M5],
LV [auth M5],
LW [auth M5],
LX [auth M5],
LY [auth M5],
LZ [auth M5],
MAA [auth M5],
MBA [auth M7],
MCA [auth MI],
MDA [auth Mf],
MEA [auth S2],
MF [auth A4],
MFA [auth S2],
MG [auth L5],
MGA [auth S3],
MH [auth L5],
MHA [auth S3],
MI [auth L5],
MIA [auth S3],
MJ [auth LV],
MJA [auth S3],
MK [auth M5],
MKA [auth S3],
ML [auth M5],
MLA [auth S3],
MM [auth M5],
MN [auth M5],
MO [auth M5],
MP [auth M5],
MQ [auth M5],
MR [auth M5],
MS [auth M5],
MT [auth M5],
MU [auth M5],
MV [auth M5],
MW [auth M5],
MX [auth M5],
MY [auth M5],
MZ [auth M5],
NAA [auth M5],
NBA [auth M7],
NCA [auth MI],
NDA [auth Mg],
NEA [auth S2],
NF [auth A5],
NFA [auth S2],
NG [auth L5],
NGA [auth S3],
NH [auth L5],
NHA [auth S3],
NI [auth L5],
NIA [auth S3],
NJA [auth S3],
NK [auth M5],
NKA [auth S3],
NL [auth M5],
NLA [auth S3],
NM [auth M5],
NN [auth M5],
NO [auth M5],
NP [auth M5],
NQ [auth M5],
NR [auth M5],
NS [auth M5],
NT [auth M5],
NU [auth M5],
NV [auth M5],
NW [auth M5],
NX [auth M5],
NY [auth M5],
NZ [auth M5],
OAA [auth M5],
OBA [auth M7],
OCA [auth MI],
ODA [auth Mg],
OEA [auth S2],
OF [auth B5],
OFA [auth S2],
OG [auth L5],
OGA [auth S3],
OH [auth L5],
OHA [auth S3],
OI [auth L5],
OIA [auth S3],
OJA [auth S3],
OK [auth M5],
OKA [auth S3],
OL [auth M5],
OLA [auth S3],
OM [auth M5],
ON [auth M5],
OO [auth M5],
OP [auth M5],
OQ [auth M5],
OR [auth M5],
OS [auth M5],
OT [auth M5],
OU [auth M5],
OV [auth M5],
OW [auth M5],
OX [auth M5],
OY [auth M5],
OZ [auth M5],
PAA [auth M5],
PBA [auth M7],
PCA [auth ML],
PDA [auth Mj],
PEA [auth S2],
PF [auth B5],
PFA [auth S2],
PG [auth L5],
PGA [auth S3],
PH [auth L5],
PHA [auth S3],
PI [auth L5],
PIA [auth S3],
PJ [auth Lj],
PJA [auth S3],
PK [auth M5],
PKA [auth S3],
PL [auth M5],
PLA [auth S3],
PM [auth M5],
PN [auth M5],
PO [auth M5],
PP [auth M5],
PQ [auth M5],
PR [auth M5],
PS [auth M5],
PT [auth M5],
PU [auth M5],
PV [auth M5],
PW [auth M5],
PX [auth M5],
PY [auth M5],
PZ [auth M5],
QAA [auth M5],
QBA [auth M7],
QCA [auth ML],
QDA [auth Mj],
QEA [auth S2],
QF [auth L5],
QFA [auth S2],
QG [auth L5],
QGA [auth S3],
QH [auth L5],
QHA [auth S3],
QI [auth L5],
QIA [auth S3],
QJA [auth S3],
QK [auth M5],
QKA [auth S3],
QL [auth M5],
QM [auth M5],
QN [auth M5],
QO [auth M5],
QP [auth M5],
QQ [auth M5],
QR [auth M5],
QS [auth M5],
QT [auth M5],
QU [auth M5],
QV [auth M5],
QW [auth M5],
QX [auth M5],
QY [auth M5],
QZ [auth M5],
RAA [auth M5],
RBA [auth M7],
RCA [auth MN],
RDA [auth Mo],
REA [auth S2],
RF [auth L5],
RFA [auth S2],
RG [auth L5],
RGA [auth S3],
RH [auth L5],
RHA [auth S3],
RI [auth L5],
RIA [auth S3],
RJA [auth S3],
RK [auth M5],
RKA [auth S3],
RL [auth M5],
RM [auth M5],
RN [auth M5],
RO [auth M5],
RP [auth M5],
RQ [auth M5],
RR [auth M5],
RS [auth M5],
RT [auth M5],
RU [auth M5],
RV [auth M5],
RW [auth M5],
RX [auth M5],
RY [auth M5],
RZ [auth M5],
SAA [auth M5],
SBA [auth M7],
SCA [auth MN],
SDA [auth Mp],
SEA [auth S2],
SF [auth L5],
SFA [auth S2],
SG [auth L5],
SGA [auth S3],
SH [auth L5],
SHA [auth S3],
SI [auth L5],
SIA [auth S3],
SJA [auth S3],
SK [auth M5],
SKA [auth S3],
SL [auth M5],
SM [auth M5],
SN [auth M5],
SO [auth M5],
SP [auth M5],
SQ [auth M5],
SR [auth M5],
SS [auth M5],
ST [auth M5],
SU [auth M5],
SV [auth M5],
SW [auth M5],
SX [auth M5],
SY [auth M5],
SZ [auth M5],
TAA [auth M5],
TBA [auth M8],
TCA [auth MN],
TDA [auth Mp],
TEA [auth S2],
TF [auth L5],
TFA [auth S2],
TG [auth L5],
TGA [auth S3],
TH [auth L5],
THA [auth S3],
TI [auth L5],
TIA [auth S3],
TJ [auth M5],
TJA [auth S3],
TK [auth M5],
TKA [auth S3],
TL [auth M5],
TM [auth M5],
TN [auth M5],
TO [auth M5],
TP [auth M5],
TQ [auth M5],
TR [auth M5],
TS [auth M5],
TT [auth M5],
TU [auth M5],
TV [auth M5],
TW [auth M5],
TX [auth M5],
TY [auth M5],
TZ [auth M5],
UAA [auth M5],
UBA [auth M8],
UCA [auth MN],
UDA [auth Mp],
UEA [auth S2],
UF [auth L5],
UFA [auth S2],
UG [auth L5],
UGA [auth S3],
UH [auth L5],
UHA [auth S3],
UI [auth L5],
UIA [auth S3],
UJ [auth M5],
UJA [auth S3],
UK [auth M5],
UKA [auth S3],
UL [auth M5],
UM [auth M5],
UN [auth M5],
UO [auth M5],
UP [auth M5],
UQ [auth M5],
UR [auth M5],
US [auth M5],
UT [auth M5],
UU [auth M5],
UV [auth M5],
UW [auth M5],
UX [auth M5],
UY [auth M5],
UZ [auth M5],
VAA [auth M5],
VBA [auth M8],
VCA [auth MO],
VDA [auth Mr],
VEA [auth S2],
VF [auth L5],
VFA [auth S2],
VG [auth L5],
VGA [auth S3],
VH [auth L5],
VHA [auth S3],
VI [auth L5],
VIA [auth S3],
VJ [auth M5],
VJA [auth S3],
VK [auth M5],
VKA [auth S3],
VL [auth M5],
VM [auth M5],
VN [auth M5],
VO [auth M5],
VP [auth M5],
VQ [auth M5],
VR [auth M5],
VS [auth M5],
VT [auth M5],
VU [auth M5],
VV [auth M5],
VW [auth M5],
VX [auth M5],
VY [auth M5],
VZ [auth M5],
WAA [auth M5],
WBA [auth M8],
WCA [auth MO],
WDA [auth Mr],
WEA [auth S2],
WF [auth L5],
WFA [auth S2],
WG [auth L5],
WGA [auth S3],
WH [auth L5],
WHA [auth S3],
WI [auth L5],
WIA [auth S3],
WJ [auth M5],
WJA [auth S3],
WK [auth M5],
WKA [auth S3],
WL [auth M5],
WM [auth M5],
WN [auth M5],
WO [auth M5],
WP [auth M5],
WQ [auth M5],
WR [auth M5],
WS [auth M5],
WT [auth M5],
WU [auth M5],
WV [auth M5],
WW [auth M5],
WX [auth M5],
WY [auth M5],
WZ [auth M5],
XAA [auth M5],
XBA [auth M8],
XCA [auth MO],
XDA [auth Mr],
XEA [auth S2],
XF [auth L5],
XFA [auth S2],
XG [auth L5],
XGA [auth S3],
XH [auth L5],
XHA [auth S3],
XI [auth L5],
XIA [auth S3],
XJ [auth M5],
XJA [auth S3],
XK [auth M5],
XKA [auth S3],
XL [auth M5],
XM [auth M5],
XN [auth M5],
XO [auth M5],
XP [auth M5],
XQ [auth M5],
XR [auth M5],
XS [auth M5],
XT [auth M5],
XU [auth M5],
XV [auth M5],
XW [auth M5],
XX [auth M5],
XY [auth M5],
XZ [auth M5],
YAA [auth M5],
YBA [auth M8],
YCA [auth MP],
YDA [auth RE],
YEA [auth S2],
YF [auth L5],
YFA [auth S2],
YG [auth L5],
YGA [auth S3],
YH [auth L5],
YHA [auth S3],
YI [auth L5],
YIA [auth S3],
YJ [auth M5],
YJA [auth S3],
YK [auth M5],
YKA [auth S3],
YL [auth M5],
YM [auth M5],
YN [auth M5],
YO [auth M5],
YP [auth M5],
YQ [auth M5],
YR [auth M5],
YS [auth M5],
YT [auth M5],
YU [auth M5],
YV [auth M5],
YW [auth M5],
YX [auth M5],
YY [auth M5],
YZ [auth M5],
ZAA [auth M5],
ZBA [auth M8],
ZCA [auth MP],
ZDA [auth RG],
ZEA [auth S2],
ZF [auth L5],
ZFA [auth S2],
ZG [auth L5],
ZGA [auth S3],
ZH [auth L5],
ZHA [auth S3],
ZI [auth L5],
ZIA [auth S3],
ZJ [auth M5],
ZJA [auth S3],
ZK [auth M5],
ZKA [auth S3],
ZL [auth M5],
ZM [auth M5],
ZN [auth M5],
ZO [auth M5],
ZP [auth M5],
ZQ [auth M5],
ZR [auth M5],
ZS [auth M5],
ZT [auth M5],
ZU [auth M5],
ZV [auth M5],
ZW [auth M5],
ZX [auth M5],
ZY [auth M5],
ZZ [auth M5]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  4 Unique
IDChains TypeFormula2D DiagramParent
V5N
Query on V5N		DB [auth MA]L-PEPTIDE LINKINGC6 H9 N3 O3HIS
HIC
Query on HIC		EB [auth MB]L-PEPTIDE LINKINGC7 H11 N3 O2HIS
MLZ
Query on MLZ		DC [auth Mb]L-PEPTIDE LINKINGC7 H16 N2 O2LYS
M3L
Query on M3L		OC [auth Mm]L-PEPTIDE LINKINGC9 H21 N2 O2LYS
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.35 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
RECONSTRUCTIONcryoSPARC

Structure Validation

View Full Validation Report



View more in-depth experimental data
Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
European Research Council (ERC)European Union--

Revision History  (Full details and data files)

  • Version 1.0: 2025-12-10
    Type: Initial release