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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 1.1 of the entry. See complete history. 

Literature

A human cell-free translation screen identifies the NT-2 mycotoxin as a ribosomal inhibitor that binds the peptidyl transferase center.

Schwaller, N., Andenmatten, D., Luginbuhl, J., Rabl, J., Baur, H., Chambon, M., Vesin, J., Turcatti, G., Karousis, E.D.

(2026) Commun Biol 9

  • DOI: https://doi.org/10.1038/s42003-026-10743-6
  • Primary Citation Related Structures: 
    29IW, 29IX, 29IY, 29IZ

  • PubMed Abstract: 

    Translation inhibitors are invaluable for probing ribosome function and therapeutic applications, but systematic discovery in human systems is limited by the lack of scalable, screening-compatible cell-free platforms. Here, we establish a robust high-throughput screening using human lysates that bypasses cellular cytotoxic effects. After screening ~28,000 small molecules, we identified known and a novel translation inhibitor, including NT-2, a trichothecene mycotoxin produced by the pathogenic Fusarium sporotrichioides. NT-2 suppressed protein synthesis in human cells and yeast lysates, while sparing translation in bacteria and intact yeast cells. Cryo-EM at 1.76 Å revealed NT-2 bound at the peptidyl transferase center of the human 60S ribosome. In addition, cryoEM classification of NT-2 treated cells shows ribosomes in an inactive eEF2/SERBP1-bound dormant state. Together, these results expose NT-2 as a previously unrecognized environmental inhibitor of mammalian protein synthesis and demonstrate the power of cell-free translation screening to reveal new inhibitors with unexpected ribosome fates.


  • Organizational Affiliation: 
    • Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Bern, Switzerland.

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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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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PHAROS:  P62424
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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UniProt GroupP32969
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Ribosomal protein uL16-likeD [auth AD]214Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000165496 
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UniProt GroupQ96L21
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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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GTEx:  ENSG00000142676 
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UniProt GroupP62913
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L13F [auth AF]211Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000167526 
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UniProt GroupP26373
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
60S ribosomal protein L14G [auth AG]215Homo sapiensMutation(s): 0 
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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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PHAROS:  Q9Y3U8
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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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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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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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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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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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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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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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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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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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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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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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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Reference Sequence
Find similar nucleic acids by:  (by identity cutoff) 
Entity ID: 43
MoleculeChains LengthOrganismImage
5.8S rRNAQA [auth DC]157Homo sapiens
Sequence Annotations
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Reference Sequence

Small Molecules

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

Query on ATP



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

Query on A1JQ4



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TJ [auth DA]Toxin NT-2
C17 H24 O7
CSYVMZMEBKUDRQ-BNWDXEGFSA-N
SPD

Query on SPD



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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



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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



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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 Modified ResidueModification TypeFormula2D Diagram
V5N
Query on V5N
HISHydroxylationC6 H9 N3 O3
MLZ
Query on MLZ
LYSMethylationC7 H16 N2 O2
HIC
Query on HIC
HISMethylationC7 H11 N3 O2

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



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
  • Version 1.1: 2026-10-07
    Changes: Data collection, Database references