4V92

Kluyveromyces lactis 80S ribosome in complex with CrPV-IRES


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 2.1 of the entry. See complete history


Literature

Initiation of Translation by Cricket Paralysis Virus Ires Requires its Translocation in the Ribosome.

Fernandez, I.S.Bai, X.Murshudov, G.Scheres, S.H.W.Ramakrishnan, V.

(2014) Cell 157: 823

  • DOI: 10.1016/j.cell.2014.04.015
  • Primary Citation of Related Structures:  
    4V91, 4V92

  • PubMed Abstract: 
  • The cricket paralysis virus internal ribosome entry site (CrPV-IRES) is a folded structure in a viral mRNA that allows initiation of translation in the absence of any host initiation factors. By using recent advances in single-particle electron cryomicroscopy, we have solved the structure of CrPV-IRES bound to the ribosome of the yeast Kluyveromyces lactis in both the canonical and rotated states at overall resolutions of 3 ...

    The cricket paralysis virus internal ribosome entry site (CrPV-IRES) is a folded structure in a viral mRNA that allows initiation of translation in the absence of any host initiation factors. By using recent advances in single-particle electron cryomicroscopy, we have solved the structure of CrPV-IRES bound to the ribosome of the yeast Kluyveromyces lactis in both the canonical and rotated states at overall resolutions of 3.7 and 3.8 Å, respectively. In both states, the pseudoknot PKI of the CrPV-IRES mimics a tRNA/mRNA interaction in the decoding center of the A site of the 40S ribosomal subunit. The structure and accompanying factor-binding data show that CrPV-IRES binding mimics a pretranslocation rather than initiation state of the ribosome. Translocation of the IRES by elongation factor 2 (eEF2) is required to bring the first codon of the mRNA into the A site and to allow the start of translation.


    Organizational Affiliation

    MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK. Electronic address: ramak@mrc-lmb.cam.ac.uk.



Macromolecules

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
US2C [auth BA]206Kluyveromyces lactisMutation(s): 0 
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
ES1D [auth BB]213Kluyveromyces lactisMutation(s): 0 
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
US5E [auth BC]216Kluyveromyces lactisMutation(s): 0 
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
US3F [auth BD]222Kluyveromyces lactisMutation(s): 0 
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
ES4G [auth BE]260Kluyveromyces lactisMutation(s): 0 
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
US7H [auth BF]206Kluyveromyces lactisMutation(s): 0 
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
ES6I [auth BG]226Kluyveromyces lactisMutation(s): 0 
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
ES7J [auth BH]184Kluyveromyces lactisMutation(s): 0 
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
ES8K [auth BI]187Kluyveromyces lactisMutation(s): 0 
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
US4L [auth BJ]179Kluyveromyces lactisMutation(s): 0 
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
ES10M [auth BK]93Kluyveromyces lactisMutation(s): 0 
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
US17N [auth BL]142Kluyveromyces lactisMutation(s): 0 
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
ES12O [auth BM]120Kluyveromyces lactisMutation(s): 0 
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
US15P [auth BN]150Kluyveromyces lactisMutation(s): 0 
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
US11Q [auth BO]127Kluyveromyces lactisMutation(s): 0 
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
US19R [auth BP]115Kluyveromyces lactisMutation(s): 0 
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
US9S [auth BQ]140Kluyveromyces lactisMutation(s): 0 
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
ES17T [auth BR]121Kluyveromyces lactisMutation(s): 0 
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
US13U [auth BS]140Kluyveromyces lactisMutation(s): 0 
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetailsImage
ES19V [auth BT]142Kluyveromyces lactisMutation(s): 0 
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetailsImage
US10W [auth BU]104Kluyveromyces lactisMutation(s): 0 
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetailsImage
ES21X [auth BV]87Kluyveromyces lactisMutation(s): 0 
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetailsImage
US8Y [auth BW]129Kluyveromyces lactisMutation(s): 0 
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetailsImage
US12Z [auth BX]142Kluyveromyces lactisMutation(s): 0 
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetailsImage
ES24AA [auth BY]134Kluyveromyces lactisMutation(s): 0 
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetailsImage
ES25BA [auth BZ]64Kluyveromyces lactisMutation(s): 0 
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetailsImage
ES26CA [auth Ba]97Kluyveromyces lactisMutation(s): 0 
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetailsImage
ES27DA [auth Bb]81Kluyveromyces lactisMutation(s): 0 
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetailsImage
ES28EA [auth Bc]63Kluyveromyces lactisMutation(s): 0 
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetailsImage
US14FA [auth Bd]52Kluyveromyces lactisMutation(s): 0 
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetailsImage
ES30GA [auth Be]55Kluyveromyces lactisMutation(s): 0 
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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetailsImage
ES31HA [auth Bf]64Kluyveromyces lactisMutation(s): 0 
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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetailsImage
RACK1IA [auth Bg]315Kluyveromyces lactisMutation(s): 0 
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Entity ID: 1
MoleculeChainsLengthOrganismImage
18S RRNAA [auth A2]1767Kluyveromyces lactis
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Entity ID: 2
MoleculeChainsLengthOrganismImage
RNA OF CRICKET-PARALYSIS-VIRUS-IRESB [auth AZ]190Cricket paralysis virus
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-07-09
    Type: Initial release
  • Version 1.1: 2014-12-10
    Changes: Other
  • Version 1.2: 2015-04-22
    Changes: Other
  • Version 2.0: 2017-08-02
    Changes: Advisory, Atomic model, Data collection, Derived calculations
  • Version 2.1: 2019-12-11
    Changes: Other