6ZVK

The Halastavi arva virus (HalV) intergenic region IRES promotes translation by the simplest possible initiation mechanism


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.49 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

The Halastavi arva Virus Intergenic Region IRES Promotes Translation by the Simplest Possible Initiation Mechanism.

Abaeva, I.S.Vicens, Q.Bochler, A.Soufari, H.Simonetti, A.Pestova, T.V.Hashem, Y.Hellen, C.U.T.

(2020) Cell Rep 33: 108476-108476

  • DOI: https://doi.org/10.1016/j.celrep.2020.108476
  • Primary Citation of Related Structures:  
    6ZVK, 7A01

  • PubMed Abstract: 

    Dicistrovirus intergenic region internal ribosomal entry sites (IGR IRESs) do not require initiator tRNA, an AUG codon, or initiation factors and jumpstart translation from the middle of the elongation cycle via formation of IRES/80S complexes resembling the pre-translocation state. eEF2 then translocates the [codon-anticodon]-mimicking pseudoknot I (PKI) from ribosomal A sites to P sites, bringing the first sense codon into the decoding center. Halastavi árva virus (HalV) contains an IGR that is related to previously described IGR IRESs but lacks domain 2, which enables these IRESs to bind to individual 40S ribosomal subunits. By using in vitro reconstitution and cryoelectron microscopy (cryo-EM), we now report that the HalV IGR IRES functions by the simplest initiation mechanism that involves binding to 80S ribosomes such that PKI is placed in the P site, so that the A site contains the first codon that is directly accessible for decoding without prior eEF2-mediated translocation of PKI.


  • Organizational Affiliation

    Department of Cell Biology, SUNY Downstate Health Sciences University, 450 Clarkson Avenue, MSC 44, Brooklyn, NY 11203, USA.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L14A [auth Z2]138Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1SZ12 (Oryctolagus cuniculus)
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN EL38E [auth p2]69Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1U001 (Oryctolagus cuniculus)
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN UL13F [auth w2]199Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G5B8P1 (Heterocephalus glaber)
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
uL22G [auth H2]153Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1SCJ6 (Oryctolagus cuniculus)
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN EL18H [auth S2]187Oryctolagus cuniculusMutation(s): 0 
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GTEx:  ENSG00000063177 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN EL19I [auth 32]180Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
uL3J [auth 52]394Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1TL06 (Oryctolagus cuniculus)
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN EL20K [auth 62]175Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
eL21L [auth 72]159Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L22M [auth 82]99Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1TSG1 (Oryctolagus cuniculus)
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
eL14N [auth k2]131Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1T6D1 (Oryctolagus cuniculus)
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L24O [auth l2]63Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN UL23P [auth m2]119Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L26Q [auth o2]134Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
uL15R [auth q2]147Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L29S [auth r2]75Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L30T [auth 13]94Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
uL4U [auth t2]362Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
eL31V [auth u2]107Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
eL32W [auth v2]128Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
eL33X [auth x2]109Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
eL34Y [auth y2]114Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN UL2Z [auth 92]244Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1TT27 (Oryctolagus cuniculus)
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
uL29AA [auth A2]122Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1SIT5 (Oryctolagus cuniculus)
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L36BA [auth B2]102Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L37CA [auth C2]86Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
ribosomal protein eL39DA [auth D2]50Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN EL40EA [auth E2]52Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
eL42FA [auth F2]104Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L5GA [auth G2]292Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
ribosomal protein eL43HA [auth I2]91Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN EL28IA [auth J2]125Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
60S acidic ribosomal protein P0JA [auth K2]198Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L10 (Predicted)KA [auth L2]102Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
Uncharacterized proteinLA [auth M2]163Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal_L6e_N domain-containing proteinMA [auth R2]35Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L6NA [auth T2]201Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
uL30OA [auth U2]225Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN EL8PA [auth V2]241Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN UL6QA [auth W2]190Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L10 (Predicted)RA [auth X2]102Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L11SA [auth Y2]169Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L13TA [auth a7]210Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L15UA [auth 12]203Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1T0C1 (Oryctolagus cuniculus)
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L27VA [auth 22]135Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1TXF6 (Oryctolagus cuniculus)
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal proteinWA [auth 42]217Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1SKZ8 (Oryctolagus cuniculus)
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal_S10 domain-containing proteinYA [auth I3]104Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for A0A5F9CX53 (Oryctolagus cuniculus)
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
40S RIBOSOMAL PROTEIN ES30ZA [auth s3]43Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for P62866 (Bos taurus)
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein S11AB [auth G3]153Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1TRM4 (Oryctolagus cuniculus)
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Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
ribosomal protein eS28BB [auth f3]64Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1TIB4 (Oryctolagus cuniculus)
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Entity ID: 56
MoleculeChains Sequence LengthOrganismDetailsImage
40S RIBOSOMAL PROTEIN ES7DB [auth P3]189Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for A6H769 (Bos taurus)
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Entity ID: 57
MoleculeChains Sequence LengthOrganismDetailsImage
40S RIBOSOMAL PROTEIN US11EB [auth a5]136Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1T1F0 (Oryctolagus cuniculus)
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Entity ID: 58
MoleculeChains Sequence LengthOrganismDetailsImage
ribosomal protein uS19FB [auth A3]127Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1U0Q2 (Oryctolagus cuniculus)
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Entity ID: 59
MoleculeChains Sequence LengthOrganismDetailsImage
40S RIBOSOMAL PROTEIN US9GB [auth B3]141Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1SGX4 (Oryctolagus cuniculus)
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Entity ID: 60
MoleculeChains Sequence LengthOrganismDetailsImage
40S RIBOSOMAL PROTEIN ES17HB [auth C3]129Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1TU13 (Oryctolagus cuniculus)
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Entity ID: 61
MoleculeChains Sequence LengthOrganismDetailsImage
40S RIBOSOMAL PROTEIN ES21IB [auth D3]83Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for A0A1Z5KTU7 (Ornithodoros moubata)
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Entity ID: 62
MoleculeChains Sequence LengthOrganismDetailsImage
ribosomal protein uS13JB [auth G5]137Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1TPG3 (Oryctolagus cuniculus)
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Entity ID: 63
MoleculeChains Sequence LengthOrganismDetailsImage
40S RIBOSOMAL PROTEIN ES19KB [auth H5]141Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1TN62 (Oryctolagus cuniculus)
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Entity ID: 64
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein S15aLB [auth J5]129Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1TG89 (Oryctolagus cuniculus)
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Entity ID: 65
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S24MB [auth I5]126Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for A0A5F9CBF4 (Oryctolagus cuniculus)
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Entity ID: 66
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S27NB [auth L3]83Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1TZ76 (Oryctolagus cuniculus)
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Entity ID: 67
MoleculeChains Sequence LengthOrganismDetailsImage
ribosomal protein eS25OB [auth M3]75Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1TDB3 (Oryctolagus cuniculus)
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Entity ID: 68
MoleculeChains Sequence LengthOrganismDetailsImage
40S RIBOSOMAL PROTEIN ES26PB [auth O3]98Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for Q56JV1 (Bos taurus)
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Entity ID: 69
MoleculeChains Sequence LengthOrganismDetailsImage
40S RIBOSOMAL PROTEIN ES31QB [auth Q3]69Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for P79781 (Gallus gallus)
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Entity ID: 70
MoleculeChains Sequence LengthOrganismDetailsImage
ribosomal protein RACK1RB [auth a3]313Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1SJB4 (Oryctolagus cuniculus)
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Entity ID: 71
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein S23SB [auth T3]141Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1SZ47 (Oryctolagus cuniculus)
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Entity ID: 72
MoleculeChains Sequence LengthOrganismDetailsImage
40S_SA_C domain-containing proteinTB [auth U3]208Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1TJH8 (Oryctolagus cuniculus)
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Entity ID: 73
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S3aUB [auth V3]213Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1SS70 (Oryctolagus cuniculus)
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Entity ID: 74
MoleculeChains Sequence LengthOrganismDetailsImage
S5 DRBM domain-containing proteinVB [auth W3]218Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 75
MoleculeChains Sequence LengthOrganismDetailsImage
60s ribosomal protein l41WB [auth X3]23Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for A0A087WNH4 (Oryctolagus cuniculus)
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Entity ID: 76
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein S3XB [auth Y3]227Oryctolagus cuniculusMutation(s): 0 
EC: 4.2.99.18
UniProt
Find proteins for G1TNM3 (Oryctolagus cuniculus)
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Entity ID: 77
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S4YB [auth j3]262Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1TK17 (Oryctolagus cuniculus)
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Entity ID: 78
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein S5ZB [auth N3]191Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for U3KMN4 (Oryctolagus cuniculus)
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Entity ID: 79
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S6AC [auth b3]237Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1TM55 (Oryctolagus cuniculus)
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Entity ID: 80
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S8BC [auth c3]206Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1TJW1 (Oryctolagus cuniculus)
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Entity ID: 81
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein S9 (Predicted)CC [auth d3]185Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for B7NZS8 (Oryctolagus cuniculus)
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Entity ID: 82
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S12DC [auth e3]124Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1SFR8 (Oryctolagus cuniculus)
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Entity ID: 83
MoleculeChains Sequence LengthOrganismDetailsImage
ribosomal protein uS15EC [auth F3]150Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1SP51 (Oryctolagus cuniculus)
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Entity ID: 84
MoleculeChains Sequence LengthOrganismDetailsImage
S10_plectin domain-containing proteinFC [auth E3]98Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1T168 (Oryctolagus cuniculus)
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Entity ID: 85
MoleculeChains Sequence LengthOrganismDetailsImage
ribosomal protein uS14GC [auth H3]53Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1U7M4 (Oryctolagus cuniculus)
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Entity ID: 2
MoleculeChains LengthOrganismImage
28S RIBOSOMAL RNAB [auth e2]3,920Oryctolagus cuniculus
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Entity ID: 3
MoleculeChains LengthOrganismImage
5S RIBOSOMAL RNAC [auth d2]120Oryctolagus cuniculus
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Entity ID: 4
MoleculeChains LengthOrganismImage
5.8S RIBOSOMAL RNAD [auth h2]156Oryctolagus cuniculus
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Entity ID: 50
MoleculeChains LengthOrganismImage
INTERNAL RIBOSOME ENTRY SITEXA [auth E1]153Halastavi arva RNA virus
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Entity ID: 55
MoleculeChains LengthOrganismImage
18S RIBOSOMAL RNACB [auth K3]1,869Oryctolagus cuniculus
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.49 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM122602
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI123406
French National Research AgencyFranceANR-14-ACHN-0024
French National Research AgencyFranceANR-11-LABX-0057_NETARN
European Research Council (ERC)FranceERC-2017-STG #759120

Revision History  (Full details and data files)

  • Version 1.0: 2020-12-23
    Type: Initial release
  • Version 1.1: 2024-05-01
    Changes: Data collection, Database references