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 29IW | pdb_000029iw

Human monosomes with bound toxin NT-2, focus on 60S subunit. Cells treated with NT-2.

  • 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: 1.77 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: 2,563.79 kDa 
  • Atom Count: 143,501 
  • Modeled Residue Count: 10,126 
  • Deposited Residue Count: 12,533 
  • Unique protein chains: 41
  • Unique nucleic acid chains: 3

Macromolecules


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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL30A [auth AA]248Homo sapiensMutation(s): 0 
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Find proteins for P18124 (Homo sapiens)
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PHAROS:  P18124
GTEx:  ENSG00000147604 
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UniProt GroupP18124
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L7aB [auth AB]266Homo sapiensMutation(s): 0 
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Find proteins for P62424 (Homo sapiens)
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GTEx:  ENSG00000148303 
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L9C [auth AC]192Homo sapiensMutation(s): 0 
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Find proteins for P32969 (Homo sapiens)
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GTEx:  ENSG00000163682 
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Ribosomal protein uL16-likeD [auth AD]214Homo sapiensMutation(s): 0 
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Find proteins for Q96L21 (Homo sapiens)
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GTEx:  ENSG00000165496 
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L11E [auth AE]178Homo sapiensMutation(s): 0 
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Find proteins for P62913 (Homo sapiens)
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PHAROS:  P62913
GTEx:  ENSG00000142676 
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L13F [auth AF]211Homo sapiensMutation(s): 0 
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Find proteins for P26373 (Homo sapiens)
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GTEx:  ENSG00000167526 
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L14G [auth AG]215Homo sapiensMutation(s): 0 
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Find proteins for P50914 (Homo sapiens)
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PHAROS:  P50914
GTEx:  ENSG00000188846 
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Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L15H [auth AH]204Homo sapiensMutation(s): 0 
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Find proteins for P61313 (Homo sapiens)
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GTEx:  ENSG00000174748 
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Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L13aI [auth AI]203Homo sapiensMutation(s): 0 
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Find proteins for P40429 (Homo sapiens)
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PHAROS:  P40429
GTEx:  ENSG00000142541 
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Entity ID: 10
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L17J [auth AJ]184Homo sapiensMutation(s): 0 
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Find proteins for P18621 (Homo sapiens)
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PHAROS:  P18621
GTEx:  ENSG00000265681 
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Entity ID: 11
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L18K [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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Entity ID: 12
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L19L [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: 13
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L18aM [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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Entity ID: 14
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L21N [auth AN]160Homo sapiensMutation(s): 0 
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Find proteins for P46778 (Homo sapiens)
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GTEx:  ENSG00000122026 
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Entity ID: 15
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L22O [auth AO]128Homo sapiensMutation(s): 0 
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Find proteins for P35268 (Homo sapiens)
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GTEx:  ENSG00000116251 
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Entity ID: 16
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L23P [auth AP]140Homo sapiensMutation(s): 0 
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Find proteins for P62829 (Homo sapiens)
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GTEx:  ENSG00000125691 
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Entity ID: 17
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L24Q [auth AQ]157Homo sapiensMutation(s): 0 
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Find proteins for P83731 (Homo sapiens)
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GTEx:  ENSG00000114391 
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Entity ID: 18
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L23aR [auth AR]156Homo sapiensMutation(s): 0 
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Find proteins for P62750 (Homo sapiens)
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GTEx:  ENSG00000198242 
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Entity ID: 19
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L26S [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: 20
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L27T [auth AT]136Homo sapiensMutation(s): 0 
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Find proteins for P61353 (Homo sapiens)
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GTEx:  ENSG00000131469 
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Entity ID: 21
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL15U [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: 22
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L29V [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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Entity ID: 23
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L30W [auth AW]115Homo sapiensMutation(s): 0 
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Find proteins for P62888 (Homo sapiens)
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GTEx:  ENSG00000156482 
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Entity ID: 24
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L31X [auth AX]125Homo sapiensMutation(s): 0 
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Find proteins for P62899 (Homo sapiens)
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GTEx:  ENSG00000071082 
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Entity ID: 25
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L32Y [auth AY]135Homo sapiensMutation(s): 0 
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Find proteins for P62910 (Homo sapiens)
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GTEx:  ENSG00000144713 
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Entity ID: 26
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL33Z [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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Entity ID: 27
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L34AA [auth Aa]117Homo sapiensMutation(s): 0 
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Find proteins for P49207 (Homo sapiens)
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GTEx:  ENSG00000109475 
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Entity ID: 28
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L35BA [auth Ab]123Homo sapiensMutation(s): 0 
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Find proteins for P42766 (Homo sapiens)
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GTEx:  ENSG00000136942 
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Entity ID: 29
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L36CA [auth Ac]105Homo sapiensMutation(s): 0 
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Find proteins for Q9Y3U8 (Homo sapiens)
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GTEx:  ENSG00000130255 
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Entity ID: 30
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL37DA [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: 31
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L38EA [auth Ae]70Homo sapiensMutation(s): 0 
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Find proteins for P63173 (Homo sapiens)
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GTEx:  ENSG00000172809 
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Entity ID: 32
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L39FA [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: 33
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL40GA [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: 34
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L36aHA [auth Ah]106Homo sapiensMutation(s): 0 
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Find proteins for P83881 (Homo sapiens)
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GTEx:  ENSG00000241343 
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Entity ID: 35
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L37aIA [auth Ai]92Homo sapiensMutation(s): 0 
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PHAROS:  P61513
GTEx:  ENSG00000197756 
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Entity ID: 36
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L28JA [auth Aj]137Homo sapiensMutation(s): 0 
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Find proteins for P46779 (Homo sapiens)
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GTEx:  ENSG00000108107 
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Entity ID: 37
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL3KA [auth BA]403Homo sapiensMutation(s): 0 
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Find proteins for P39023 (Homo sapiens)
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GTEx:  ENSG00000100316 
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Entity ID: 38
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L4LA [auth BB]427Homo sapiensMutation(s): 0 
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Find proteins for P36578 (Homo sapiens)
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GTEx:  ENSG00000174444 
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Entity ID: 39
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L5MA [auth BC]297Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000122406 
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Entity ID: 40
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL6NA [auth BD]288Homo sapiensMutation(s): 0 
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Find proteins for Q02878 (Homo sapiens)
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GTEx:  ENSG00000089009 
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Entity ID: 44
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL2RA [auth DD]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: 41
MoleculeChains LengthOrganismImage
28S rRNAOA [auth DA]5,069Homo sapiens
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Entity ID: 42
MoleculeChains LengthOrganismImage
5S rRNAPA [auth DB]120Homo sapiens
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Entity ID: 43
MoleculeChains LengthOrganismImage
5.8S rRNAQA [auth DC]157Homo sapiens
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Reference Sequence

Small Molecules

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

Query on ATP


Download:Ideal Coordinates CCD File
QB [auth DA]ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
A1JQ4(
Subject of Investigation/LOI)

Query on A1JQ4


Download:Ideal Coordinates CCD File
TJ [auth DA]Toxin NT-2
C17 H24 O7
CSYVMZMEBKUDRQ-BNWDXEGFSA-N
SPD

Query on SPD


Download:Ideal Coordinates CCD File
KB [auth DA]
LB [auth DA]
MB [auth DA]
NB [auth DA]
OB [auth DA]
KB [auth DA],
LB [auth DA],
MB [auth DA],
NB [auth DA],
OB [auth DA],
PB [auth DA]
SPERMIDINE
C7 H19 N3
ATHGHQPFGPMSJY-UHFFFAOYSA-N
PUT

Query on PUT


Download:Ideal Coordinates CCD File
GB [auth DA],
HB [auth DA],
IB [auth DA],
JB [auth DA],
UJ [auth DB]		1,4-DIAMINOBUTANE
C4 H12 N2
KIDHWZJUCRJVML-UHFFFAOYSA-N
ZN

Query on ZN


Download:Ideal Coordinates CCD File
AB [auth Ad],
CB [auth Ag],
DB [auth Ah],
EB [auth Ai],
ZA [auth Aa]		ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
K

Query on K


Download:Ideal Coordinates CCD File
AC [auth DA]
AD [auth DA]
BC [auth DA]
BD [auth DA]
BK [auth DD]
AC [auth DA],
AD [auth DA],
BC [auth DA],
BD [auth DA],
BK [auth DD],
CC [auth DA],
CD [auth DA],
CK [auth DD],
DC [auth DA],
DD [auth DA],
EC [auth DA],
ED [auth DA],
FC [auth DA],
FD [auth DA],
GC [auth DA],
HC [auth DA],
IC [auth DA],
JC [auth DA],
KC [auth DA],
LC [auth DA],
MC [auth DA],
NC [auth DA],
OC [auth DA],
PC [auth DA],
QC [auth DA],
RB [auth DA],
RC [auth DA],
SB [auth DA],
SC [auth DA],
TB [auth DA],
TC [auth DA],
UA [auth AM],
UB [auth DA],
UC [auth DA],
VA [auth AN],
VB [auth DA],
VC [auth DA],
WB [auth DA],
WC [auth DA],
XB [auth DA],
XC [auth DA],
XJ [auth DC],
YB [auth DA],
YC [auth DA],
ZB [auth DA],
ZC [auth DA]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
MG

Query on MG


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

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 1.77 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
Swiss National Science FoundationSwitzerlandCRSK-3_220624

Revision History  (Full details and data files)

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