6P5N

Structure of a mammalian 80S ribosome in complex with a single translocated Israeli Acute Paralysis Virus IRES and eRF1

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history. 


Literature

The Israeli acute paralysis virus IRES captures host ribosomes by mimicking a ribosomal state with hybrid tRNAs.

Acosta-Reyes, F., Neupane, R., Frank, J., Fernandez, I.S.

(2019) EMBO J 38: e102226-e102226

  • DOI: 10.15252/embj.2019102226
  • Primary Citation of Related Structures:  
    6P4G, 6P4H, 6P5K, 6P5N, 6P5J, 6P5I

  • PubMed Abstract: 

    • Colony collapse disorder (CCD) is a multi-faceted syndrome decimating bee populations worldwide, and a group of viruses of the widely distributed Dicistroviridae family have been identified as a causing agent of CCD. This family of viruses employs non-co ...

    Colony collapse disorder (CCD) is a multi-faceted syndrome decimating bee populations worldwide, and a group of viruses of the widely distributed Dicistroviridae family have been identified as a causing agent of CCD. This family of viruses employs non-coding RNA sequences, called internal ribosomal entry sites (IRESs), to precisely exploit the host machinery for viral protein production. Using single-particle cryo-electron microscopy (cryo-EM), we have characterized how the IRES of Israeli acute paralysis virus (IAPV) intergenic region captures and redirects translating ribosomes toward viral RNA messages. We reconstituted two in vitro reactions targeting a pre-translocation and a post-translocation state of the IAPV-IRES in the ribosome, allowing us to identify six structures using image processing classification methods. From these, we reconstructed the trajectory of IAPV-IRES from the early small subunit recruitment to the final post-translocated state in the ribosome. An early commitment of IRES/ribosome complexes for global pre-translocation mimicry explains the high efficiency observed for this IRES. Efforts directed toward fighting CCD by targeting the IAPV-IRES using RNA-interference technology are underway, and the structural framework presented here may assist in further refining these approaches.

    Organizational Affiliation: 

    Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA.



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Entity ID: 4
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uL2 AA257Oryctolagus cuniculusMutation(s): 0 
Gene Names: ZNF34
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uL3 AB402Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL3
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uL4 AC392Oryctolagus cuniculusMutation(s): 0 
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uL18 AD297Oryctolagus cuniculusMutation(s): 0 
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eL6 AE291Oryctolagus cuniculusMutation(s): 0 
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L30 AF249Oryctolagus cuniculusMutation(s): 0 
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eL8 AG242Oryctolagus cuniculusMutation(s): 0 
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uL6 AH192Oryctolagus cuniculusMutation(s): 0 
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uL16 AI214Oryctolagus cuniculusMutation(s): 0 
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L14e AM198Oryctolagus cuniculusMutation(s): 0 
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uL22 AP184Oryctolagus cuniculusMutation(s): 0 
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eL20 AS176Oryctolagus cuniculusMutation(s): 0 
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eL21 AT160Oryctolagus cuniculusMutation(s): 0 
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eL22 AU128Oryctolagus cuniculusMutation(s): 0 
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uL14 AV140Oryctolagus cuniculusMutation(s): 0 
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eL24 AW157Oryctolagus cuniculusMutation(s): 0 
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eL23 AX156Oryctolagus cuniculusMutation(s): 0 
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uL24 AY145Oryctolagus cuniculusMutation(s): 0 
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eL27 AZ136Oryctolagus cuniculusMutation(s): 0 
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uL15 Aa148Oryctolagus cuniculusMutation(s): 0 
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eL29 Ab226Oryctolagus cuniculusMutation(s): 0 
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eL30 Ac115Oryctolagus cuniculusMutation(s): 0 
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eL31 Ad125Oryctolagus cuniculusMutation(s): 0 
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eL32 Ae135Oryctolagus cuniculusMutation(s): 0 
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eL33 Af110Oryctolagus cuniculusMutation(s): 0 
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eL34 Ag126Oryctolagus cuniculusMutation(s): 0 
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eL35 Ah123Oryctolagus cuniculusMutation(s): 0 
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eL36 Ai105Oryctolagus cuniculusMutation(s): 0 
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eL37 Aj97Oryctolagus cuniculusMutation(s): 0 
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eL38 Ak70Oryctolagus cuniculusMutation(s): 0 
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eL39 Al51Oryctolagus cuniculusMutation(s): 0 
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eL40 Am52Oryctolagus cuniculusMutation(s): 0 
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eL41 An25Oryctolagus cuniculusMutation(s): 0 
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eL42 Ao106Oryctolagus cuniculusMutation(s): 0 
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eL43 Ap92Oryctolagus cuniculusMutation(s): 0 
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eL28 Ar137Oryctolagus cuniculusMutation(s): 0 
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eS1 C264Oryctolagus cuniculusMutation(s): 0 
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uS5 D255Oryctolagus cuniculusMutation(s): 0 
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uS3 E281Oryctolagus cuniculusMutation(s): 0 
EC: 4.2.99.18
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eS4 F263Oryctolagus cuniculusMutation(s): 0 
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uS7 G204Oryctolagus cuniculusMutation(s): 0 
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uS17 M158Oryctolagus cuniculusMutation(s): 0 
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eS12 N132Oryctolagus cuniculusMutation(s): 0 
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uS15 O151Oryctolagus cuniculusMutation(s): 0 
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uS11 P151Oryctolagus cuniculusMutation(s): 0 
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uS19 Q145Oryctolagus cuniculusMutation(s): 0 
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uS9 R172Oryctolagus cuniculusMutation(s): 0 
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eS17 S135Oryctolagus cuniculusMutation(s): 0 
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uS13 T152Oryctolagus cuniculusMutation(s): 0 
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eS19 U145Oryctolagus cuniculusMutation(s): 0 
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uS10 V119Oryctolagus cuniculusMutation(s): 0 
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eS21 W83Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS21
Find proteins for G1TM82 (Oryctolagus cuniculus)
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Entity ID: 70
MoleculeChainsSequence LengthOrganismDetailsImage
uS8 X130Oryctolagus cuniculusMutation(s): 0 
Find proteins for G1TG89 (Oryctolagus cuniculus)
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Entity ID: 71
MoleculeChainsSequence LengthOrganismDetailsImage
uS12 Y143Oryctolagus cuniculusMutation(s): 0 
Find proteins for G1SZ47 (Oryctolagus cuniculus)
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Entity ID: 72
MoleculeChainsSequence LengthOrganismDetailsImage
eS24 Z134Oryctolagus cuniculusMutation(s): 0 
Find proteins for G1T3D8 (Oryctolagus cuniculus)
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Entity ID: 73
MoleculeChainsSequence LengthOrganismDetailsImage
eS25 a125Oryctolagus cuniculusMutation(s): 0 
Find proteins for G1TDB3 (Oryctolagus cuniculus)
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Entity ID: 74
MoleculeChainsSequence LengthOrganismDetailsImage
eS26 b115Oryctolagus cuniculusMutation(s): 0 
Find proteins for G1TFE8 (Oryctolagus cuniculus)
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Entity ID: 75
MoleculeChainsSequence LengthOrganismDetailsImage
eS27 c84Oryctolagus cuniculusMutation(s): 0 
Find proteins for G1TZ76 (Oryctolagus cuniculus)
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Entity ID: 76
MoleculeChainsSequence LengthOrganismDetailsImage
eS28 d69Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS28
Find proteins for G1TIB4 (Oryctolagus cuniculus)
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Entity ID: 77
MoleculeChainsSequence LengthOrganismDetailsImage
eS29 e56Oryctolagus cuniculusMutation(s): 0 
Find proteins for G1U7M4 (Oryctolagus cuniculus)
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Entity ID: 78
MoleculeChainsSequence LengthOrganismDetailsImage
eS30 f133Oryctolagus cuniculusMutation(s): 0 
Find proteins for G1T8A2 (Oryctolagus cuniculus)
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Entity ID: 79
MoleculeChainsSequence LengthOrganismDetailsImage
eS31 g156Oryctolagus cuniculusMutation(s): 0 
Find proteins for G1SK22 (Oryctolagus cuniculus)
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Entity ID: 80
MoleculeChainsSequence LengthOrganismDetailsImage
RACK1 h317Oryctolagus cuniculusMutation(s): 0 
Find proteins for G1SJB4 (Oryctolagus cuniculus)
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Entity ID: 81
MoleculeChainsSequence LengthOrganismDetailsImage
Eukaryotic peptide chain release factor subunit 1 Aq437Homo sapiensMutation(s): 0 
Gene Names: ETF1, ERF1, RF1, SUP45L1
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Entity ID: 1
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28S rRNA53594Oryctolagus cuniculus
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Entity ID: 2
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5S rRNA7119Oryctolagus cuniculus
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Entity ID: 3
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5.8S rRNA8156Oryctolagus cuniculus
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Entity ID: 47
MoleculeChainsLengthOrganismImage
18S rRNA21869Oryctolagus cuniculus
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Entity ID: 82
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IAPV-IRES1251Israeli acute paralysis virus
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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View more in-depth experimental data

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM029169

Revision History 

  • Version 1.0: 2019-09-25
    Type: Initial release
  • Version 1.1: 2019-10-30
    Changes: Data collection, Database references
  • Version 1.2: 2019-11-20
    Changes: Database references
  • Version 1.3: 2020-01-08
    Changes: Author supporting evidence