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 1.0 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: 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 ...

    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. Electronic address: christopher.hellen@downstate.edu.



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Ribosomal protein L14A [auth Z2]138Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL14
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60S RIBOSOMAL PROTEIN EL38E [auth p2]69Oryctolagus cuniculusMutation(s): 0 
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60S RIBOSOMAL PROTEIN UL13F [auth w2]199Oryctolagus cuniculusMutation(s): 0 
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uL22G [auth H2]153Oryctolagus cuniculusMutation(s): 0 
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60S RIBOSOMAL PROTEIN EL18H [auth S2]187Oryctolagus cuniculusMutation(s): 0 
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uL3J [auth 52]394Oryctolagus cuniculusMutation(s): 0 
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eL21L [auth 72]159Oryctolagus cuniculusMutation(s): 0 
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Ribosomal protein L22M [auth 82]99Oryctolagus cuniculusMutation(s): 0 
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eL14N [auth k2]131Oryctolagus cuniculusMutation(s): 0 
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60S RIBOSOMAL PROTEIN UL23P [auth m2]119Oryctolagus cuniculusMutation(s): 0 
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uL15R [auth q2]147Oryctolagus cuniculusMutation(s): 0 
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60S ribosomal protein L29S [auth r2]75Oryctolagus cuniculusMutation(s): 0 
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uL4U [auth t2]362Oryctolagus cuniculusMutation(s): 0 
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eL31V [auth u2]107Oryctolagus cuniculusMutation(s): 0 
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eL33X [auth x2]109Oryctolagus cuniculusMutation(s): 0 
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eL34Y [auth y2]114Oryctolagus cuniculusMutation(s): 0 
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60S RIBOSOMAL PROTEIN UL2Z [auth 92]244Oryctolagus cuniculusMutation(s): 0 
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uL29AA [auth A2]122Oryctolagus cuniculusMutation(s): 0 
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60S ribosomal protein L36BA [auth B2]102Oryctolagus cuniculusMutation(s): 0 
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Ribosomal protein L37CA [auth C2]86Oryctolagus cuniculusMutation(s): 0 
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ribosomal protein eL39DA [auth D2]50Oryctolagus cuniculusMutation(s): 0 
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60S RIBOSOMAL PROTEIN EL40EA [auth E2]52Oryctolagus cuniculusMutation(s): 0 
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eL42FA [auth F2]104Oryctolagus cuniculusMutation(s): 0 
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60S ribosomal protein L5GA [auth G2]292Oryctolagus cuniculusMutation(s): 0 
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ribosomal protein eL43HA [auth I2]91Oryctolagus cuniculusMutation(s): 0 
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60S RIBOSOMAL PROTEIN EL28IA [auth J2]125Oryctolagus cuniculusMutation(s): 0 
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60S acidic ribosomal protein P0JA [auth K2]198Oryctolagus cuniculusMutation(s): 0 
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Ribosomal protein L10 (Predicted)KA [auth L2]102Oryctolagus cuniculusMutation(s): 0 
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Ribosomal_L6e_N domain-containing proteinMA [auth R2]35Oryctolagus cuniculusMutation(s): 0 
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60S ribosomal protein L6NA [auth T2]201Oryctolagus cuniculusMutation(s): 0 
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uL30OA [auth U2]225Oryctolagus cuniculusMutation(s): 0 
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60S RIBOSOMAL PROTEIN EL8PA [auth V2]241Oryctolagus cuniculusMutation(s): 0 
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60S RIBOSOMAL PROTEIN UL6QA [auth W2]190Oryctolagus cuniculusMutation(s): 0 
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Ribosomal protein L10 (Predicted)RA [auth X2]102Oryctolagus cuniculusMutation(s): 0 
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Ribosomal protein L11SA [auth Y2]169Oryctolagus cuniculusMutation(s): 0 
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60S ribosomal protein L13TA [auth a7]210Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 47
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Ribosomal protein L15UA [auth 12]203Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1T0C1 (Oryctolagus cuniculus)
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Entity ID: 48
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60S ribosomal protein L27VA [auth 22]135Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1TXF6 (Oryctolagus cuniculus)
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Entity ID: 49
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Ribosomal proteinWA [auth 42]217Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 51
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Ribosomal_S10 domain-containing proteinYA [auth I3]104Oryctolagus cuniculusMutation(s): 0 
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Find proteins for A0A5F9CX53 (Oryctolagus cuniculus)
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Entity ID: 52
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40S RIBOSOMAL PROTEIN ES30ZA [auth s3]43Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 53
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Ribosomal protein S11AB [auth G3]153Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS11
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Entity ID: 54
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ribosomal protein eS28BB [auth f3]64Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS28
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Entity ID: 56
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40S RIBOSOMAL PROTEIN ES7DB [auth P3]189Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 57
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40S RIBOSOMAL PROTEIN US11EB [auth a5]136Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 58
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ribosomal protein uS19FB [auth A3]127Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS15
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Entity ID: 59
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40S RIBOSOMAL PROTEIN US9GB [auth B3]141Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 60
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40S RIBOSOMAL PROTEIN ES17HB [auth C3]129Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 61
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40S RIBOSOMAL PROTEIN ES21IB [auth D3]83Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 62
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ribosomal protein uS13JB [auth G5]137Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 63
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40S RIBOSOMAL PROTEIN ES19KB [auth H5]141Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 64
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Ribosomal protein S15aLB [auth J5]129Oryctolagus cuniculusMutation(s): 0 
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40S ribosomal protein S24MB [auth I5]126Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 66
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40S ribosomal protein S27NB [auth L3]83Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 67
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ribosomal protein eS25OB [auth M3]75Oryctolagus cuniculusMutation(s): 0 
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40S RIBOSOMAL PROTEIN ES26PB [auth O3]98Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 69
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40S RIBOSOMAL PROTEIN ES31QB [auth Q3]69Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 70
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ribosomal protein RACK1RB [auth a3]313Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 71
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Ribosomal protein S23SB [auth T3]141Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 72
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40S_SA_C domain-containing proteinTB [auth U3]208Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 73
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40S ribosomal protein S3aUB [auth V3]213Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS3A
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Entity ID: 74
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S5 DRBM domain-containing proteinVB [auth W3]218Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 75
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60s ribosomal protein l41WB [auth X3]23Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 76
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Ribosomal protein S3XB [auth Y3]227Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS3
EC: 4.2.99.18
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Entity ID: 77
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40S ribosomal protein S4YB [auth j3]262Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 78
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Ribosomal protein S5ZB [auth N3]191Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS5
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Entity ID: 79
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40S ribosomal protein S6AC [auth b3]237Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 80
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40S ribosomal protein S8BC [auth c3]206Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 81
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Ribosomal protein S9 (Predicted)CC [auth d3]185Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS9
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Entity ID: 82
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40S ribosomal protein S12DC [auth e3]124Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS12
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Entity ID: 83
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ribosomal protein uS15EC [auth F3]150Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 84
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S10_plectin domain-containing proteinFC [auth E3]98Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 85
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ribosomal protein uS14GC [auth H3]53Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 2
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28S RIBOSOMAL RNAB [auth e2]3920Oryctolagus cuniculus
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5S RIBOSOMAL RNAC [auth d2]120Oryctolagus cuniculus
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5.8S RIBOSOMAL RNAD [auth h2]156Oryctolagus cuniculus
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Entity ID: 50
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INTERNAL RIBOSOME ENTRY SITEXA [auth E1]153Halastavi arva RNA virus
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Entity ID: 55
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18S RIBOSOMAL RNACB [auth K3]1869Oryctolagus cuniculus
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Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
HC [auth C2],
IC [auth E2],
JC [auth F2],
KC [auth I2],
LC [auth O3],
HC [auth C2],
IC [auth E2],
JC [auth F2],
KC [auth I2],
LC [auth O3],
MC [auth H3]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
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