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 29IY | pdb_000029iy

Human monosomes, focus on 60S subunit; control.

  • Classification: RIBOSOME
  • Organism(s): Homo sapiens
  • Mutation(s): No 

  • Deposited: 2026-03-15 Released: 2026-09-30 
  • Deposition Author(s): Rabl, J., Karousis, E.D.
  • Funding Organization(s): Swiss National Science Foundation

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.36 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

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

Literature

Toxin NT-2 bound to human ribosome

Rabl, J., Karousis, E.D.

To be published.

Macromolecule Content 

  • Total Structure Weight: 2,321.28 kDa 
  • Atom Count: 125,014 
  • Modeled Residue Count: 8,221 
  • Deposited Residue Count: 10,418 
  • Unique protein chains: 31
  • Unique nucleic acid chains: 3

Macromolecules


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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L29A [auth AV]159Homo sapiensMutation(s): 0 
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Find proteins for P47914 (Homo sapiens)
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GTEx:  ENSG00000162244 
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UniProt GroupP47914
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L30B [auth AW]115Homo sapiensMutation(s): 0 
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Find proteins for P62888 (Homo sapiens)
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PHAROS:  P62888
GTEx:  ENSG00000156482 
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L31C [auth AX]125Homo sapiensMutation(s): 0 
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Find proteins for P62899 (Homo sapiens)
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PHAROS:  P62899
GTEx:  ENSG00000071082 
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L32D [auth AY]135Homo sapiensMutation(s): 0 
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Find proteins for P62910 (Homo sapiens)
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PHAROS:  P62910
GTEx:  ENSG00000144713 
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL33E [auth AZ]110Homo sapiensMutation(s): 0 
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Find proteins for P18077 (Homo sapiens)
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PHAROS:  P18077
GTEx:  ENSG00000182899 
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UniProt GroupP18077
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L34F [auth Aa]117Homo sapiensMutation(s): 0 
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Find proteins for P49207 (Homo sapiens)
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PHAROS:  P49207
GTEx:  ENSG00000109475 
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L35G [auth Ab]123Homo sapiensMutation(s): 0 
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Find proteins for P42766 (Homo sapiens)
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PHAROS:  P42766
GTEx:  ENSG00000136942 
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Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L36H [auth Ac]105Homo sapiensMutation(s): 0 
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Find proteins for Q9Y3U8 (Homo sapiens)
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PHAROS:  Q9Y3U8
GTEx:  ENSG00000130255 
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Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL37I [auth Ad]97Homo sapiensMutation(s): 0 
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Find proteins for P61927 (Homo sapiens)
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PHAROS:  P61927
GTEx:  ENSG00000145592 
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Entity ID: 10
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L38J [auth Ae]70Homo sapiensMutation(s): 0 
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Find proteins for P63173 (Homo sapiens)
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PHAROS:  P63173
GTEx:  ENSG00000172809 
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Entity ID: 11
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L39K [auth Af]51Homo sapiensMutation(s): 0 
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Find proteins for P62891 (Homo sapiens)
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GTEx:  ENSG00000198918 
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Entity ID: 12
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL40L [auth Ag]128Homo sapiensMutation(s): 0 
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Find proteins for P62987 (Homo sapiens)
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PHAROS:  P62987
GTEx:  ENSG00000221983 
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Entity ID: 13
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L36aM [auth Ah]106Homo sapiensMutation(s): 0 
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Find proteins for P83881 (Homo sapiens)
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PHAROS:  P83881
GTEx:  ENSG00000241343 
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Entity ID: 14
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L37aN [auth Ai]92Homo sapiensMutation(s): 0 
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Find proteins for P61513 (Homo sapiens)
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PHAROS:  P61513
GTEx:  ENSG00000197756 
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Entity ID: 15
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L28O [auth Aj]137Homo sapiensMutation(s): 0 
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Find proteins for P46779 (Homo sapiens)
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PHAROS:  P46779
GTEx:  ENSG00000108107 
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Entity ID: 16
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL3P [auth BA]403Homo sapiensMutation(s): 0 
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Find proteins for P39023 (Homo sapiens)
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PHAROS:  P39023
GTEx:  ENSG00000100316 
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Entity ID: 17
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L4Q [auth BB]427Homo sapiensMutation(s): 0 
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Find proteins for P36578 (Homo sapiens)
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PHAROS:  P36578
GTEx:  ENSG00000174444 
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Entity ID: 18
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L5R [auth BC]297Homo sapiensMutation(s): 0 
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Find proteins for P46777 (Homo sapiens)
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PHAROS:  P46777
GTEx:  ENSG00000122406 
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Entity ID: 19
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL6S [auth BD]288Homo sapiensMutation(s): 0 
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Find proteins for Q02878 (Homo sapiens)
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PHAROS:  Q02878
GTEx:  ENSG00000089009 
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Entity ID: 23
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL2W [auth CD]257Homo sapiensMutation(s): 0 
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Find proteins for P62917 (Homo sapiens)
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GTEx:  ENSG00000161016 
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Entity ID: 24
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L18X [auth AK]188Homo sapiensMutation(s): 0 
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Find proteins for Q07020 (Homo sapiens)
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PHAROS:  Q07020
GTEx:  ENSG00000063177 
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UniProt GroupQ07020
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Entity ID: 25
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L19Y [auth AL]196Homo sapiensMutation(s): 0 
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Find proteins for P84098 (Homo sapiens)
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PHAROS:  P84098
GTEx:  ENSG00000108298 
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Entity ID: 26
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L18aZ [auth AM]176Homo sapiensMutation(s): 0 
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Find proteins for Q02543 (Homo sapiens)
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GTEx:  ENSG00000105640 
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UniProt GroupQ02543
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Entity ID: 27
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L21AA [auth AN]160Homo sapiensMutation(s): 0 
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Find proteins for P46778 (Homo sapiens)
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PHAROS:  P46778
GTEx:  ENSG00000122026 
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UniProt GroupP46778
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Entity ID: 28
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L22BA [auth AO]128Homo sapiensMutation(s): 0 
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Find proteins for P35268 (Homo sapiens)
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PHAROS:  P35268
GTEx:  ENSG00000116251 
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Entity ID: 29
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L23CA [auth AP]140Homo sapiensMutation(s): 0 
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Find proteins for P62829 (Homo sapiens)
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PHAROS:  P62829
GTEx:  ENSG00000125691 
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Entity ID: 30
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L24DA [auth AQ]157Homo sapiensMutation(s): 0 
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Find proteins for P83731 (Homo sapiens)
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PHAROS:  P83731
GTEx:  ENSG00000114391 
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Entity ID: 31
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L23aEA [auth AR]156Homo sapiensMutation(s): 0 
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Find proteins for P62750 (Homo sapiens)
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PHAROS:  P62750
GTEx:  ENSG00000198242 
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Entity ID: 32
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L26FA [auth AS]145Homo sapiensMutation(s): 0 
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Find proteins for P61254 (Homo sapiens)
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PHAROS:  P61254
GTEx:  ENSG00000161970 
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Entity ID: 33
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L27GA [auth AT]136Homo sapiensMutation(s): 0 
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Find proteins for P61353 (Homo sapiens)
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PHAROS:  P61353
GTEx:  ENSG00000131469 
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Entity ID: 34
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL15HA [auth AU]148Homo sapiensMutation(s): 0 
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Find proteins for P46776 (Homo sapiens)
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PHAROS:  P46776
GTEx:  ENSG00000166441 
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Entity ID: 20
MoleculeChains LengthOrganismImage
28S rRNAT [auth CA]5,069Homo sapiens
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Entity ID: 21
MoleculeChains LengthOrganismImage
5S rRNAU [auth CB]120Homo sapiens
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Entity ID: 22
MoleculeChains LengthOrganismImage
5.8S rRNAV [auth CC]157Homo sapiens
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Small Molecules

Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ATP

Query on ATP


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PA [auth Ah]ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
SPM

Query on SPM


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CB [auth CA],
DB [auth CA],
EB [auth CA],
FB [auth CA],
GB [auth CA]		SPERMINE
C10 H26 N4
PFNFFQXMRSDOHW-UHFFFAOYSA-N
SPD

Query on SPD


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AB [auth CA]
BB [auth CA]
WA [auth CA]
XA [auth CA]
YA [auth CA]
AB [auth CA],
BB [auth CA],
WA [auth CA],
XA [auth CA],
YA [auth CA],
ZA [auth CA]
SPERMIDINE
C7 H19 N3
ATHGHQPFGPMSJY-UHFFFAOYSA-N
PUT

Query on PUT


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MJ [auth CB],
SA [auth CA],
TA [auth CA],
UA [auth CA],
VA [auth CA]		1,4-DIAMINOBUTANE
C4 H12 N2
KIDHWZJUCRJVML-UHFFFAOYSA-N
ZN

Query on ZN


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KA [auth Aa],
LA [auth Ad],
NA [auth Ag],
OA [auth Ah],
QA [auth Ai]		ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
K

Query on K


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AC [auth CA]
BC [auth CA]
CC [auth CA]
DC [auth CA]
EC [auth CA]
AC [auth CA],
BC [auth CA],
CC [auth CA],
DC [auth CA],
EC [auth CA],
FC [auth CA],
GC [auth CA],
HB [auth CA],
HC [auth CA],
IB [auth CA],
IC [auth CA],
JB [auth CA],
JC [auth CA],
KB [auth CA],
KC [auth CA],
LB [auth CA],
LC [auth CA],
MB [auth CA],
MC [auth CA],
NB [auth CA],
NC [auth CA],
OB [auth CA],
OC [auth CA],
PB [auth CA],
PC [auth CA],
QB [auth CA],
QC [auth CA],
RB [auth CA],
RC [auth CA],
SB [auth CA],
SC [auth CA],
SJ [auth CD],
TB [auth CA],
TC [auth CA],
TJ [auth CD],
UB [auth CA],
UC [auth CA],
UJ [auth AM],
VB [auth CA],
VC [auth CA],
VJ [auth AN],
WB [auth CA],
WJ [auth AP],
XB [auth CA],
YB [auth CA],
ZB [auth CA]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
MG

Query on MG


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AD [auth CA]
AE [auth CA]
AF [auth CA]
AG [auth CA]
AH [auth CA]
AD [auth CA],
AE [auth CA],
AF [auth CA],
AG [auth CA],
AH [auth CA],
AI [auth CA],
AJ [auth CA],
BD [auth CA],
BE [auth CA],
BF [auth CA],
BG [auth CA],
BH [auth CA],
BI [auth CA],
BJ [auth CA],
CD [auth CA],
CE [auth CA],
CF [auth CA],
CG [auth CA],
CH [auth CA],
CI [auth CA],
CJ [auth CA],
DD [auth CA],
DE [auth CA],
DF [auth CA],
DG [auth CA],
DH [auth CA],
DI [auth CA],
DJ [auth CA],
ED [auth CA],
EE [auth CA],
EF [auth CA],
EG [auth CA],
EH [auth CA],
EI [auth CA],
EJ [auth CA],
FD [auth CA],
FE [auth CA],
FF [auth CA],
FG [auth CA],
FH [auth CA],
FI [auth CA],
FJ [auth CA],
GD [auth CA],
GE [auth CA],
GF [auth CA],
GG [auth CA],
GH [auth CA],
GI [auth CA],
GJ [auth CA],
HD [auth CA],
HE [auth CA],
HF [auth CA],
HG [auth CA],
HH [auth CA],
HI [auth CA],
HJ [auth CA],
IA [auth AY],
ID [auth CA],
IE [auth CA],
IF [auth CA],
IG [auth CA],
IH [auth CA],
II [auth CA],
IJ [auth CA],
JA [auth AZ],
JD [auth CA],
JE [auth CA],
JF [auth CA],
JG [auth CA],
JH [auth CA],
JI [auth CA],
JJ [auth CA],
KD [auth CA],
KE [auth CA],
KF [auth CA],
KG [auth CA],
KH [auth CA],
KI [auth CA],
KJ [auth CA],
LD [auth CA],
LE [auth CA],
LF [auth CA],
LG [auth CA],
LH [auth CA],
LI [auth CA],
LJ [auth CA],
MA [auth Ad],
MD [auth CA],
ME [auth CA],
MF [auth CA],
MG [auth CA],
MH [auth CA],
MI [auth CA],
ND [auth CA],
NE [auth CA],
NF [auth CA],
NG [auth CA],
NH [auth CA],
NI [auth CA],
NJ [auth CB],
OD [auth CA],
OE [auth CA],
OF [auth CA],
OG [auth CA],
OH [auth CA],
OI [auth CA],
OJ [auth CB],
PD [auth CA],
PE [auth CA],
PF [auth CA],
PG [auth CA],
PH [auth CA],
PI [auth CA],
PJ [auth CC],
QD [auth CA],
QE [auth CA],
QF [auth CA],
QG [auth CA],
QH [auth CA],
QI [auth CA],
QJ [auth CC],
RA [auth BA],
RD [auth CA],
RE [auth CA],
RF [auth CA],
RG [auth CA],
RH [auth CA],
RI [auth CA],
RJ [auth CC],
SD [auth CA],
SE [auth CA],
SF [auth CA],
SG [auth CA],
SH [auth CA],
SI [auth CA],
TD [auth CA],
TE [auth CA],
TF [auth CA],
TG [auth CA],
TH [auth CA],
TI [auth CA],
UD [auth CA],
UE [auth CA],
UF [auth CA],
UG [auth CA],
UH [auth CA],
UI [auth CA],
VD [auth CA],
VE [auth CA],
VF [auth CA],
VG [auth CA],
VH [auth CA],
VI [auth CA],
WC [auth CA],
WD [auth CA],
WE [auth CA],
WF [auth CA],
WG [auth CA],
WH [auth CA],
WI [auth CA],
XC [auth CA],
XD [auth CA],
XE [auth CA],
XF [auth CA],
XG [auth CA],
XH [auth CA],
XI [auth CA],
XJ [auth AP],
YC [auth CA],
YD [auth CA],
YE [auth CA],
YF [auth CA],
YG [auth CA],
YH [auth CA],
YI [auth CA],
ZC [auth CA],
ZD [auth CA],
ZE [auth CA],
ZF [auth CA],
ZG [auth CA],
ZH [auth CA],
ZI [auth CA]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  3 Unique
IDChains TypeFormula2D DiagramParent
MLZ
Query on MLZ		L [auth Ag]L-PEPTIDE LINKINGC7 H16 N2 O2LYS
HIC
Query on HIC		P [auth BA]L-PEPTIDE LINKINGC7 H11 N3 O2HIS
V5N
Query on V5N		W [auth CD]L-PEPTIDE LINKINGC6 H9 N3 O3HIS

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.36 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC

Structure Validation

View Full Validation Report



View more in-depth experimental data

Entry History 

& Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Swiss National Science FoundationSwitzerlandCRSK-3_220624

Revision History  (Full details and data files)

  • Version 1.0: 2026-09-30
    Type: Initial release