6P5K

Structure of a mammalian 80S ribosome in complex with the Israeli Acute Paralysis Virus IRES (Class 3)


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 1.3 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:  
    6P4H, 6P5K, 6P5N, 6P5J, 6P5I, 6P4G

  • 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 no ...

    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
MoleculeChainsSequence LengthOrganismDetailsImage
uL2AA257Oryctolagus cuniculusMutation(s): 0 
Gene Names: ZNF34
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Entity ID: 5
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uL3AB403Oryctolagus cuniculusMutation(s): 0 
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uL4AC392Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL4
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eL6AE291Oryctolagus cuniculusMutation(s): 0 
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uL30AF249Oryctolagus cuniculusMutation(s): 0 
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eL8AG242Oryctolagus cuniculusMutation(s): 0 
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uL6AH192Oryctolagus cuniculusMutation(s): 0 
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uL16AI214Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL10
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uL11AJ178Oryctolagus cuniculusMutation(s): 0 
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eL13AL211Oryctolagus cuniculusMutation(s): 0 
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L14eAM198Oryctolagus cuniculusMutation(s): 0 
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eL15AN204Oryctolagus cuniculusMutation(s): 0 
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uL13AO203Oryctolagus cuniculusMutation(s): 0 
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uL22AP184Oryctolagus cuniculusMutation(s): 0 
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eL18AQ188Oryctolagus cuniculusMutation(s): 0 
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eL19AR196Oryctolagus cuniculusMutation(s): 0 
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eL20AS176Oryctolagus cuniculusMutation(s): 0 
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eL21AT160Oryctolagus cuniculusMutation(s): 0 
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eL22AU128Oryctolagus cuniculusMutation(s): 0 
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eL24AW157Oryctolagus cuniculusMutation(s): 0 
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eL23AX156Oryctolagus cuniculusMutation(s): 0 
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uL24AY145Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL26
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eL27AZ136Oryctolagus cuniculusMutation(s): 0 
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uL15Aa148Oryctolagus cuniculusMutation(s): 0 
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eL29Ab226Oryctolagus cuniculusMutation(s): 0 
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eL30Ac115Oryctolagus cuniculusMutation(s): 0 
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eL31Ad125Oryctolagus cuniculusMutation(s): 0 
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eL32Ae135Oryctolagus cuniculusMutation(s): 0 
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eL33Af110Oryctolagus cuniculusMutation(s): 0 
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eL34Ag126Oryctolagus cuniculusMutation(s): 0 
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eL35Ah123Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 37
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eL36Ai105Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 38
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eL37Aj97Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL37
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eL38Ak70Oryctolagus cuniculusMutation(s): 0 
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eL39Al51Oryctolagus cuniculusMutation(s): 0 
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eL40Am52Oryctolagus cuniculusMutation(s): 0 
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eL41An25Oryctolagus cuniculusMutation(s): 0 
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eL42Ao106Oryctolagus cuniculusMutation(s): 0 
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eL43Ap92Oryctolagus cuniculusMutation(s): 0 
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eL28Ar137Oryctolagus cuniculusMutation(s): 0 
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uL1AK217Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 48
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uS2B295Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 49
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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 
Gene Names: RPS5
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eS6H249Oryctolagus cuniculusMutation(s): 0 
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eS7I194Oryctolagus cuniculusMutation(s): 0 
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eS8J207Oryctolagus cuniculusMutation(s): 0 
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uS4K194Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS9
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eS10L149Oryctolagus cuniculusMutation(s): 0 
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uS17M158Oryctolagus cuniculusMutation(s): 0 
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eS12N132Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS12
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uS15O151Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 62
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uS11P151Oryctolagus cuniculusMutation(s): 0 
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uS19Q145Oryctolagus cuniculusMutation(s): 0 
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uS9R172Oryctolagus cuniculusMutation(s): 0 
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eS17S135Oryctolagus cuniculusMutation(s): 0 
Find proteins for G1TU13 (Oryctolagus cuniculus)
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Entity ID: 66
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uS13T152Oryctolagus cuniculusMutation(s): 0 
Find proteins for G1TPG3 (Oryctolagus cuniculus)
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Entity ID: 67
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eS19U145Oryctolagus cuniculusMutation(s): 0 
Find proteins for G1TN62 (Oryctolagus cuniculus)
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Entity ID: 68
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uS10V119Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 69
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eS21W83Oryctolagus cuniculusMutation(s): 0 
Find proteins for G1TM82 (Oryctolagus cuniculus)
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Entity ID: 70
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uS8X130Oryctolagus cuniculusMutation(s): 0 
Find proteins for G1TG89 (Oryctolagus cuniculus)
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Entity ID: 71
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uS12Y143Oryctolagus cuniculusMutation(s): 0 
Find proteins for G1SZ47 (Oryctolagus cuniculus)
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Entity ID: 72
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eS24Z134Oryctolagus cuniculusMutation(s): 0 
Find proteins for G1T3D8 (Oryctolagus cuniculus)
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Entity ID: 73
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eS25a125Oryctolagus cuniculusMutation(s): 0 
Find proteins for G1TDB3 (Oryctolagus cuniculus)
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Entity ID: 74
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eS26b115Oryctolagus cuniculusMutation(s): 0 
Find proteins for G1TFE8 (Oryctolagus cuniculus)
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Entity ID: 75
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eS27c84Oryctolagus cuniculusMutation(s): 0 
Find proteins for G1TZ76 (Oryctolagus cuniculus)
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Entity ID: 76
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eS28d69Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS28
Find proteins for G1TIB4 (Oryctolagus cuniculus)
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Entity ID: 77
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eS29e56Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 78
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eS30f133Oryctolagus cuniculusMutation(s): 0 
Find proteins for G1T8A2 (Oryctolagus cuniculus)
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Entity ID: 79
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eS31g156Oryctolagus cuniculusMutation(s): 0 
Find proteins for G1SK22 (Oryctolagus cuniculus)
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Entity ID: 80
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RACK1h317Oryctolagus cuniculusMutation(s): 0 
Find proteins for G1SJB4 (Oryctolagus cuniculus)
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Entity ID: 24
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uL14AV140Oryctolagus cuniculusMutation(s): 0 
Find proteins for G1T6D1 (Oryctolagus cuniculus)
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Entity ID: 7
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uL18AD297Oryctolagus cuniculusMutation(s): 0 
Find proteins for G1SYJ6 (Oryctolagus cuniculus)
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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
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18S rRNA21869Oryctolagus cuniculus
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Entity ID: 81
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IAPV-IRES1253Israeli acute paralysis virus
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 

  • 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