6D9J

Mammalian 80S ribosome with a double translocated CrPV-IRES, P-sitetRNA 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 1.2 of the entry. See complete history


Literature

Dual tRNA mimicry in the Cricket Paralysis Virus IRES uncovers an unexpected similarity with the Hepatitis C Virus IRES.

Pisareva, V.P.Pisarev, A.V.Fernandez, I.S.

(2018) Elife 7

  • DOI: 10.7554/eLife.34062
  • Primary Citation of Related Structures:  
    6D9J, 6D90

  • PubMed Abstract: 
  • Co-opting the cellular machinery for protein production is a compulsory requirement for viruses. The Cricket Paralysis Virus employs an Internal Ribosomal Entry Site (CrPV-IRES) to express its structural genes in the late stage of infection. Ribosome ...

    Co-opting the cellular machinery for protein production is a compulsory requirement for viruses. The Cricket Paralysis Virus employs an Internal Ribosomal Entry Site (CrPV-IRES) to express its structural genes in the late stage of infection. Ribosome hijacking is achieved by a sophisticated use of molecular mimicry to tRNA and mRNA, employed to manipulate intrinsically dynamic components of the ribosome. Binding and translocation through the ribosome is required for this IRES to initiate translation. We report two structures, solved by single particle electron cryo-microscopy (cryoEM), of a double translocated CrPV-IRES with aminoacyl-tRNA in the peptidyl site (P site) of the ribosome. CrPV-IRES adopts a previously unseen conformation, mimicking the acceptor stem of a canonical E site tRNA. The structures suggest a mechanism for the positioning of the first aminoacyl-tRNA shared with the distantly related Hepatitis C Virus IRES.


    Organizational Affiliation

    Department of Biochemistry and Molecular Biophysics, Columbia University, New York, United States.



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Entity ID: 1
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uL2A257Oryctolagus cuniculusMutation(s): 0 
Gene Names: ZNF34
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uL3B403Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPL3
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uL4C392Oryctolagus cuniculusMutation(s): 0 
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uL18D297Oryctolagus cuniculusMutation(s): 0 
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eL6E291Oryctolagus cuniculusMutation(s): 0 
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uL30F249Oryctolagus cuniculusMutation(s): 0 
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eL8G242Oryctolagus cuniculusMutation(s): 0 
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uL16I214Oryctolagus cuniculusMutation(s): 0 
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uL11J178Oryctolagus cuniculusMutation(s): 0 
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eL13L211Oryctolagus cuniculusMutation(s): 0 
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eL14M198Oryctolagus cuniculusMutation(s): 0 
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uL22P187Oryctolagus cuniculusMutation(s): 0 
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eL21T160Oryctolagus cuniculusMutation(s): 0 
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uL14V140Oryctolagus cuniculusMutation(s): 0 
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eL24W157Oryctolagus cuniculusMutation(s): 0 
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eL27Z136Oryctolagus cuniculusMutation(s): 0 
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eL29b226Oryctolagus cuniculusMutation(s): 0 
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eL30c115Oryctolagus cuniculusMutation(s): 0 
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eL31d125Oryctolagus cuniculusMutation(s): 0 
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eL32e135Oryctolagus cuniculusMutation(s): 0 
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eL33f110Oryctolagus cuniculusMutation(s): 0 
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eL35h123Oryctolagus cuniculusMutation(s): 0 
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eL36i105Oryctolagus cuniculusMutation(s): 0 
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eL37j97Oryctolagus cuniculusMutation(s): 0 
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eL38k69Oryctolagus cuniculusMutation(s): 0 
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eL39l51Oryctolagus cuniculusMutation(s): 0 
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eL40m52Oryctolagus cuniculusMutation(s): 0 
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eL41n25Oryctolagus cuniculusMutation(s): 0 
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eL42o106Oryctolagus cuniculusMutation(s): 0 
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eL43p92Oryctolagus cuniculusMutation(s): 0 
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eL28r137Oryctolagus cuniculusMutation(s): 0 
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uL10s303Oryctolagus cuniculusMutation(s): 0 
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uL11t195Oryctolagus cuniculusMutation(s): 0 
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eS1CC264Oryctolagus cuniculusMutation(s): 0 
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uS5DD221Oryctolagus cuniculusMutation(s): 0 
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uS3EE281Oryctolagus cuniculusMutation(s): 0 
EC: 4.2.99.18
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uS7GG204Oryctolagus cuniculusMutation(s): 0 
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eS12NN132Oryctolagus cuniculusMutation(s): 0 
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uS15OO151Oryctolagus cuniculusMutation(s): 0 
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uS19QQ145Oryctolagus cuniculusMutation(s): 0 
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uS9RR172Oryctolagus cuniculusMutation(s): 0 
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eS17SS135Oryctolagus cuniculusMutation(s): 0 
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uS13TT152Oryctolagus cuniculusMutation(s): 0 
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eS19UU145Oryctolagus cuniculusMutation(s): 0 
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uS10VV119Oryctolagus cuniculusMutation(s): 0 
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eS21WW83Oryctolagus cuniculusMutation(s): 0 
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uS8XX130Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 73
MoleculeChainsSequence LengthOrganismDetailsImage
uS12YY143Oryctolagus cuniculusMutation(s): 0 
Find proteins for G1SZ47 (Oryctolagus cuniculus)
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Entity ID: 74
MoleculeChainsSequence LengthOrganismDetailsImage
eS24ZZ134Oryctolagus cuniculusMutation(s): 0 
Find proteins for G1T3D8 (Oryctolagus cuniculus)
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Entity ID: 75
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eS25aa125Oryctolagus cuniculusMutation(s): 0 
Find proteins for G1TDB3 (Oryctolagus cuniculus)
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Entity ID: 76
MoleculeChainsSequence LengthOrganismDetailsImage
eS26bb101Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 77
MoleculeChainsSequence LengthOrganismDetailsImage
eS27cc84Oryctolagus cuniculusMutation(s): 0 
Find proteins for G1TZ76 (Oryctolagus cuniculus)
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Entity ID: 78
MoleculeChainsSequence LengthOrganismDetailsImage
eS28dd69Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS28
Find proteins for G1TIB4 (Oryctolagus cuniculus)
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Entity ID: 79
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eS29ee56Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 80
MoleculeChainsSequence LengthOrganismDetailsImage
eS30ff133Oryctolagus cuniculusMutation(s): 0 
Find proteins for G1T8A2 (Oryctolagus cuniculus)
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Entity ID: 81
MoleculeChainsSequence LengthOrganismDetailsImage
eS31gg156Oryctolagus cuniculusMutation(s): 0 
Find proteins for G1SK22 (Oryctolagus cuniculus)
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Entity ID: 82
MoleculeChainsSequence LengthOrganismDetailsImage
RACK1hh317Oryctolagus cuniculusMutation(s): 0 
Find proteins for G1SJB4 (Oryctolagus cuniculus)
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Entity ID: 84
MoleculeChainsSequence LengthOrganismDetailsImage
eEF29856Homo sapiensMutation(s): 0 
Gene Names: EEF2EF2
Find proteins for P13639 (Homo sapiens)
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NIH Common Fund Data Resources
PHAROS  P13639
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Entity ID: 45
MoleculeChainsLengthOrganismImage
28S rRNA53594Oryctolagus cuniculus
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Entity ID: 46
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5S rRNA7119Oryctolagus cuniculus
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Entity ID: 47
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5.8S rRNA8151Oryctolagus cuniculus
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Entity ID: 49
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18S rRNA21697Oryctolagus cuniculus
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Entity ID: 83
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P-site tRNA387Escherichia coli
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Entity ID: 85
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CrPV IRES4190Cricket paralysis virus
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 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 Human Genome Research Institute (NIH/NHGRI)United StatesGM097014

Revision History 

  • Version 1.0: 2018-06-06
    Type: Initial release
  • Version 1.1: 2018-06-13
    Changes: Data collection, Database references
  • Version 1.2: 2019-12-18
    Changes: Author supporting evidence, Other