6P4H

Structure of a mammalian small ribosomal subunit in complex with the Israeli Acute Paralysis Virus IRES (Class 2)


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 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.



Macromolecules

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
uS2B295Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPSA
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
uS3E281Oryctolagus cuniculusMutation(s): 0 
EC: 4.2.99.18
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
eS4F263Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
eS8J207Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
uS17M158Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
eS12N132Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS12
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Entity ID: 16
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uS15O151Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 17
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uS11P151Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 18
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uS19Q145Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 19
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uS9R172Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 20
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eS17S135Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 22
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eS19U145Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 23
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uS10V119Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 24
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eS21W83Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 27
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eS24Z134Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 31
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eS28d69Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS28
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Entity ID: 33
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eS30f133Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 35
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RACK1h317Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 36
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eL41n25Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 10
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eS7I194Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 12
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uS4K194Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS9
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Entity ID: 13
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eS10L149Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 21
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uS13T152Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 25
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uS8X130Oryctolagus cuniculusMutation(s): 0 
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uS12Y143Oryctolagus cuniculusMutation(s): 0 
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eS25a125Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 29
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eS26b115Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 3
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eS1C264Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS3A
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Entity ID: 30
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eS27c84Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 32
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eS29e56Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 34
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eS31g156Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 4
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uS5D255Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 8
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uS7G204Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS5
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Entity ID: 9
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eS6H249Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 6
MoleculeChainsLengthOrganismImage
IAPV-IRES1253Israeli acute paralysis virus
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Entity ID: 1
MoleculeChainsLengthOrganismImage
18S rRNA21869Oryctolagus cuniculus
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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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM29169

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: 2019-11-13
    Changes: Database references
  • Version 1.3: 2020-01-08
    Changes: Author supporting evidence