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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 1.1 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: 2,321.28 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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UniProt GroupP62910
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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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Reference Sequence
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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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UniProt GroupP49207
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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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UniProt GroupQ9Y3U8
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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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UniProt GroupP62891
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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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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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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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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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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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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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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 Modified ResidueModification TypeFormula2D Diagram
MLZ
Query on MLZ
LYSMethylationC7 H16 N2 O2
HIC
Query on HIC
HISMethylationC7 H11 N3 O2
V5N
Query on V5N
HISHydroxylationC6 H9 N3 O3

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



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