9YPY | pdb_00009ypy

Ribosome with accommodated A-site tRNA, Structure V


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Structural mechanism of mRNA decoding by mammalian GTPase GTPBP1.

Susorov, D.Miscicka, A.Golovenko, D.Loveland, A.B.Zinoviev, A.Pestova, T.V.Korostelev, A.A.

(2025) Nat Commun 

  • DOI: https://doi.org/10.1038/s41467-025-66833-2
  • Primary Citation of Related Structures:  
    9YPO, 9YPS, 9YPT, 9YPV, 9YPY, 9YPZ, 9YQ0, 9YQ1

  • PubMed Abstract: 

    GTP-binding protein 1 (GTPBP1) is a widespread translational GTPase closely related to elongation factor eEF1A. The loss of GTPBP1 leads to neurodevelopmental and neurodegenerative disorders in animals. Although linked to translation and quality control mechanisms, GTPBP1 molecular functions remain largely obscure. Similarly to eEF1A, GTPBP1 delivers aminoacyl-tRNA to the ribosome, but the ensuing GTPBP1-mediated elongation is slow. Here, using cryo-EM of mammalian 80S ribosomal complexes bound to GTPBP1 and aa-tRNA with GTP or the non-hydrolysable analog GDPCP, we show that the distinct GTPBP1 architecture and interactions with tRNA underlie slow GTPBP1 dissociation after GTP hydrolysis, resulting in delayed tRNA accommodation. Slow dissociation correlates with an extended proofreading stage and higher accuracy of GTPBP1-mediated decoding, potentially allowing GTPBP1 to elicit its putative quality control functions. GTPBP1 visualization provides the foundation for mapping and elucidating GTPBP1 mutations associated with human diseases.


  • Organizational Affiliation
    • RNA Therapeutics Institute, UMass Chan Medical School, Worcester, MA, USA.

Macromolecules

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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L8E [auth A]257Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L3F [auth B]403Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1TL06 (Oryctolagus cuniculus)
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L4G [auth C]425Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1SVW5 (Oryctolagus cuniculus)
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL18H [auth D]297Oryctolagus cuniculusMutation(s): 0 
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Find proteins for P19949 (Oryctolagus cuniculus)
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L6I [auth E]291Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L7aJ [auth G]319Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L9K [auth H]192Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L10L [auth I]214Oryctolagus cuniculusMutation(s): 0 
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Find proteins for B7NZQ2 (Oryctolagus cuniculus)
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L11M [auth J]178Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1TUB8 (Oryctolagus cuniculus)
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L7N [auth K]247Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L13O [auth L]211Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1TPV0 (Oryctolagus cuniculus)
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L14P [auth M]218Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1SZ12 (Oryctolagus cuniculus)
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L15Q [auth N]204Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL13R [auth O]203Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1TVS8 (Oryctolagus cuniculus)
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL22S [auth P]184Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1SCJ6 (Oryctolagus cuniculus)
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L18T [auth Q]188Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L19U [auth R]196Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1TJR3 (Oryctolagus cuniculus)
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L18aV [auth S]176Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1TTY7 (Oryctolagus cuniculus)
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
eL21W [auth T]160Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1SHQ2 (Oryctolagus cuniculus)
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
eL22X [auth U]128Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1TSG1 (Oryctolagus cuniculus)
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L23Y [auth V]140Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1T6D1 (Oryctolagus cuniculus)
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
eL24Z [auth W]157Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1SE28 (Oryctolagus cuniculus)
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
eL23AA [auth X]156Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1SE76 (Oryctolagus cuniculus)
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
uL24BA [auth Y]145Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1SQH0 (Oryctolagus cuniculus)
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L27CA [auth Z]136Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L27aDA [auth a]148Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL29EA [auth b]245Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
eL30FA [auth c]115Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1TDL2 (Oryctolagus cuniculus)
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
eL31GA [auth d]125Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L32HA [auth e]135Oryctolagus cuniculusMutation(s): 0 
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Find proteins for A0AAA9WVN6 (Oryctolagus cuniculus)
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
eL33IA [auth f]110Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1SF08 (Oryctolagus cuniculus)
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL34JA [auth g]116Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
eL35KA [auth h]123Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L36LA [auth i]105Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
eL38MA [auth k]70Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
eL39NA [auth l]51Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquitin A-52 residue ribosomal protein fusion product 1OA [auth m]102Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
eL41PA [auth n]25Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for A0A087WNH4 (Oryctolagus cuniculus)
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL42QA [auth o]106Oryctolagus cuniculusMutation(s): 0 
UniProt
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
eL43RA [auth p]92Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1SY53 (Oryctolagus cuniculus)
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
eL28SA [auth r]137Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1U7L1 (Oryctolagus cuniculus)
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
uS2 (SA)TA [auth AA]295Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1TLT8 (Oryctolagus cuniculus)
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S3aUA [auth BB]264Oryctolagus cuniculusMutation(s): 0 
UniProt
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS5VA [auth CC]293Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for O18789 (Bos taurus)
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein S3WA [auth DD]243Oryctolagus cuniculusMutation(s): 0 
EC: 4.2.99.18
UniProt
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
eS4 (S4 X isoform)XA [auth EE]263Oryctolagus cuniculusMutation(s): 0 
UniProt
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein S5YA [auth FF]204Oryctolagus cuniculusMutation(s): 0 
UniProt
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S6ZA [auth GG]249Oryctolagus cuniculusMutation(s): 0 
UniProt
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S7AB [auth HH]194Oryctolagus cuniculusMutation(s): 0 
UniProt
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Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S8BB [auth II]208Oryctolagus cuniculusMutation(s): 0 
UniProt
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Entity ID: 55
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein S9 (Predicted)CB [auth JJ]194Oryctolagus cuniculusMutation(s): 0 
UniProt
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Entity ID: 56
MoleculeChains Sequence LengthOrganismDetailsImage
S10_plectin domain-containing proteinDB [auth KK]165Oryctolagus cuniculusMutation(s): 0 
UniProt
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Entity ID: 57
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein S11EB [auth LL]158Oryctolagus cuniculusMutation(s): 0 
UniProt
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Entity ID: 58
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S12FB [auth MM]132Oryctolagus cuniculusMutation(s): 0 
UniProt
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Entity ID: 59
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein S13GB [auth NN]151Oryctolagus cuniculusMutation(s): 0 
UniProt
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Entity ID: 60
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS11HB [auth OO]168Oryctolagus cuniculusMutation(s): 0 
UniProt
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Entity ID: 61
MoleculeChains Sequence LengthOrganismDetailsImage
uS19IB [auth PP]145Oryctolagus cuniculusMutation(s): 0 
UniProt
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Entity ID: 62
MoleculeChains Sequence LengthOrganismDetailsImage
uS9JB [auth QQ]146Oryctolagus cuniculusMutation(s): 0 
UniProt
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Entity ID: 63
MoleculeChains Sequence LengthOrganismDetailsImage
eS17KB [auth RR]135Oryctolagus cuniculusMutation(s): 0 
UniProt
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Entity ID: 64
MoleculeChains Sequence LengthOrganismDetailsImage
uS13LB [auth SS]152Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 65
MoleculeChains Sequence LengthOrganismDetailsImage
eS19MB [auth TT]145Oryctolagus cuniculusMutation(s): 0 
UniProt
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Entity ID: 66
MoleculeChains Sequence LengthOrganismDetailsImage
uS10NB [auth UU]119Oryctolagus cuniculusMutation(s): 0 
UniProt
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Entity ID: 67
MoleculeChains Sequence LengthOrganismDetailsImage
eS21OB [auth VV]83Oryctolagus cuniculusMutation(s): 0 
UniProt
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Entity ID: 68
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein S15aPB [auth WW]130Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1TG89 (Oryctolagus cuniculus)
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Entity ID: 69
MoleculeChains Sequence LengthOrganismDetailsImage
uS12QB [auth XX]143Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1SZ47 (Oryctolagus cuniculus)
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Entity ID: 70
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S24RB [auth YY]130Oryctolagus cuniculusMutation(s): 0 
UniProt
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Entity ID: 71
MoleculeChains Sequence LengthOrganismDetailsImage
eS25SB [auth ZZ]125Oryctolagus cuniculusMutation(s): 0 
UniProt
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Entity ID: 72
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S26TB [auth aa]115Oryctolagus cuniculusMutation(s): 0 
UniProt
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Entity ID: 73
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S27UB [auth bb]84Oryctolagus cuniculusMutation(s): 0 
UniProt
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Entity ID: 74
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein S28VB [auth cc]69Oryctolagus cuniculusMutation(s): 0 
UniProt
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Entity ID: 75
MoleculeChains Sequence LengthOrganismDetailsImage
eS29WB [auth dd]56Oryctolagus cuniculusMutation(s): 0 
UniProt
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Entity ID: 76
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S30XB [auth ee]133Oryctolagus cuniculusMutation(s): 0 
UniProt
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Entity ID: 77
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein S27aYB [auth ff]156Oryctolagus cuniculusMutation(s): 0 
UniProt
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Entity ID: 78
MoleculeChains Sequence LengthOrganismDetailsImage
RACK1ZB [auth gg]317Oryctolagus cuniculusMutation(s): 0 
UniProt
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Entity ID: 82
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L37DC [auth j]97Oryctolagus cuniculusMutation(s): 0 
UniProt
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Entity ID: 1
MoleculeChains LengthOrganismImage
28S ribosomal RNAA [auth 5]3,601Oryctolagus cuniculus
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Entity ID: 2
MoleculeChains LengthOrganismImage
5S ribosomal RNAB [auth 7]120Oryctolagus cuniculus
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Entity ID: 3
MoleculeChains LengthOrganismImage
5.8S ribosomal RNAC [auth 8]156Oryctolagus cuniculus
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Entity ID: 4
MoleculeChains LengthOrganismImage
18S ribosomal RNAD [auth 9]1,869Oryctolagus cuniculus
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Entity ID: 79
MoleculeChains LengthOrganismImage
MF mRNAAC [auth 10]185Oryctolagus cuniculus
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Entity ID: 80
MoleculeChains LengthOrganismImage
Phe-tRNABC [auth 12]76Saccharomyces cerevisiae
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Entity ID: 81
MoleculeChains LengthOrganismImage
Met-tRNACC [auth 13],
EC [auth 11]
75Homo sapiens
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Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GTP
Query on GTP

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LC [auth 12]GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
ATP
Query on ATP

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NC [auth 13],
QC [auth 11]
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
PHE
Query on PHE

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MC [auth 12]PHENYLALANINE
C9 H11 N O2
COLNVLDHVKWLRT-QMMMGPOBSA-N
MET
Query on MET

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OC [auth 13]METHIONINE
C5 H11 N O2 S
FFEARJCKVFRZRR-BYPYZUCNSA-N
SPD
Query on SPD

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FC [auth 5]SPERMIDINE
C7 H19 N3
ATHGHQPFGPMSJY-UHFFFAOYSA-N
ZN
Query on ZN

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GC [auth g]
HC [auth m]
IC [auth o]
JC [auth p]
KC [auth dd]
GC [auth g],
HC [auth m],
IC [auth o],
JC [auth p],
KC [auth dd],
PC [auth j]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION
MODEL REFINEMENTPHENIX1.21.1_5286

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35GM127094
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35GM122602

Revision History  (Full details and data files)

  • Version 1.0: 2025-12-24
    Type: Initial release