6P5I

Structure of a mammalian 80S ribosome in complex with the Israeli Acute Paralysis Virus IRES (Class 1)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.4 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-coding RNA sequences, called internal ribosomal entry sites (IRESs), to precisely exploit the host machinery for viral protein production ...

    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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uS2B295Oryctolagus cuniculusMutation(s): 0 
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eS1C264Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS3A
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uS5D255Oryctolagus cuniculusMutation(s): 0 
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uS3E281Oryctolagus cuniculusMutation(s): 0 
EC: 4.2.99.18
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eS4F263Oryctolagus cuniculusMutation(s): 0 
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uS7G204Oryctolagus cuniculusMutation(s): 0 
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eS6H249Oryctolagus cuniculusMutation(s): 0 
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eS21W83Oryctolagus cuniculusMutation(s): 0 
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eS24Z134Oryctolagus cuniculusMutation(s): 0 
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eS25AA [auth a]125Oryctolagus cuniculusMutation(s): 0 
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eS26BA [auth b]115Oryctolagus cuniculusMutation(s): 0 
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eS27CA [auth c]84Oryctolagus cuniculusMutation(s): 0 
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eS28DA [auth d]69Oryctolagus cuniculusMutation(s): 0 
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eS29EA [auth e]56Oryctolagus cuniculusMutation(s): 0 
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eS30FA [auth f]133Oryctolagus cuniculusMutation(s): 0 
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eS31GA [auth g]156Oryctolagus cuniculusMutation(s): 0 
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RACK1HA [auth h]317Oryctolagus cuniculusMutation(s): 0 
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uL2MA [auth AA]257Oryctolagus cuniculusMutation(s): 0 
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uL3NA [auth AB]403Oryctolagus cuniculusMutation(s): 0 
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uL4OA [auth AC]392Oryctolagus cuniculusMutation(s): 0 
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uL18PA [auth AD]297Oryctolagus cuniculusMutation(s): 0 
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eL6QA [auth AE]291Oryctolagus cuniculusMutation(s): 0 
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uL30RA [auth AF]249Oryctolagus cuniculusMutation(s): 0 
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eL8SA [auth AG]242Oryctolagus cuniculusMutation(s): 0 
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uL6TA [auth AH]192Oryctolagus cuniculusMutation(s): 0 
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uL16UA [auth AI]214Oryctolagus cuniculusMutation(s): 0 
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uL11VA [auth AJ]178Oryctolagus cuniculusMutation(s): 0 
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eL13WA [auth AL]211Oryctolagus cuniculusMutation(s): 0 
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L14eXA [auth AM]198Oryctolagus cuniculusMutation(s): 0 
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eL15YA [auth AN]204Oryctolagus cuniculusMutation(s): 0 
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uL22AB [auth AP]184Oryctolagus cuniculusMutation(s): 0 
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eL21EB [auth AT]160Oryctolagus cuniculusMutation(s): 0 
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eL22FB [auth AU]128Oryctolagus cuniculusMutation(s): 0 
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uL14GB [auth AV]140Oryctolagus cuniculusMutation(s): 0 
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eL24HB [auth AW]157Oryctolagus cuniculusMutation(s): 0 
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eL23IB [auth AX]156Oryctolagus cuniculusMutation(s): 0 
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uL24JB [auth AY]145Oryctolagus cuniculusMutation(s): 0 
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eL27KB [auth AZ]136Oryctolagus cuniculusMutation(s): 0 
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uL15LB [auth Aa]148Oryctolagus cuniculusMutation(s): 0 
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eL29MB [auth Ab]226Oryctolagus cuniculusMutation(s): 0 
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eL30NB [auth Ac]115Oryctolagus cuniculusMutation(s): 0 
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eL31OB [auth Ad]125Oryctolagus cuniculusMutation(s): 0 
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eL32PB [auth Ae]135Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 69
MoleculeChainsSequence LengthOrganismDetailsImage
eL33QB [auth Af]110Oryctolagus cuniculusMutation(s): 0 
Find proteins for G1SF08 (Oryctolagus cuniculus)
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Entity ID: 70
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eL34RB [auth Ag]126Oryctolagus cuniculusMutation(s): 0 
Find proteins for G1U945 (Oryctolagus cuniculus)
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Entity ID: 71
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eL35SB [auth Ah]123Oryctolagus cuniculusMutation(s): 0 
Find proteins for G1SIT5 (Oryctolagus cuniculus)
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Entity ID: 72
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eL36TB [auth Ai]105Oryctolagus cuniculusMutation(s): 0 
Find proteins for G1TTQ5 (Oryctolagus cuniculus)
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Entity ID: 73
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eL37UB [auth Aj]97Oryctolagus cuniculusMutation(s): 0 
Find proteins for U3KPD5 (Oryctolagus cuniculus)
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Entity ID: 74
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eL38VB [auth Ak]69Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 75
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eL39WB [auth Al]51Oryctolagus cuniculusMutation(s): 0 
Find proteins for G1TTN1 (Oryctolagus cuniculus)
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Entity ID: 76
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eL40XB [auth Am]52Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 77
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eL41YB [auth An]25Oryctolagus cuniculusMutation(s): 0 
Find proteins for A0A087WNH4 (Oryctolagus cuniculus)
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Entity ID: 78
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eL42ZB [auth Ao]106Oryctolagus cuniculusMutation(s): 0 
Find proteins for G1U344 (Oryctolagus cuniculus)
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Entity ID: 79
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eL43AC [auth Ap]92Oryctolagus cuniculusMutation(s): 0 
Find proteins for G1SY53 (Oryctolagus cuniculus)
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Entity ID: 80
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eL28BC [auth Ar]137Oryctolagus cuniculusMutation(s): 0 
Find proteins for G1U7L1 (Oryctolagus cuniculus)
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Entity ID: 81
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uL1CC [auth AK]217Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 1
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18S rRNAA [auth 2]1869Oryctolagus cuniculus
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Entity ID: 35
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IAPV-IRESIA [auth 1]253Israeli acute paralysis virus
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Entity ID: 36
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28S rRNAJA [auth 5]3594Oryctolagus cuniculus
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Entity ID: 37
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5S rRNAKA [auth 7]119Oryctolagus cuniculus
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Entity ID: 38
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5.8S rRNALA [auth 8]156Oryctolagus cuniculus
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 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 StatesGM029169

Revision History  (Full details and data files)

  • Version 1.0: 2019-09-18
    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
  • Version 1.4: 2020-02-26
    Changes: Database references, Source and taxonomy