4V91

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: 4
MoleculeChainsSequence LengthOrganismDetailsImage
UL2D [auth A]254Kluyveromyces lactisMutation(s): 0 
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
UL3E [auth B]387Kluyveromyces lactisMutation(s): 0 
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
UL4F [auth C]362Kluyveromyces lactisMutation(s): 0 
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
UL18G [auth D]297Kluyveromyces lactisMutation(s): 0 
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
EL6H [auth E]176Kluyveromyces lactisMutation(s): 0 
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
UL30I [auth F]244Kluyveromyces lactisMutation(s): 0 
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
EL8J [auth G]256Kluyveromyces lactisMutation(s): 0 
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
UL6K [auth H]191Kluyveromyces lactisMutation(s): 0 
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
UL16L [auth I]221Kluyveromyces lactisMutation(s): 0 
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
UL5M [auth J]174Kluyveromyces lactisMutation(s): 0 
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
EL13N [auth L]199Kluyveromyces lactisMutation(s): 0 
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
EL14O [auth M]138Kluyveromyces lactisMutation(s): 0 
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
EL15P [auth N]204Kluyveromyces lactisMutation(s): 0 
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
UL13Q [auth O]398Kluyveromyces lactisMutation(s): 0 
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Entity ID: 18
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UL22R [auth P]184Kluyveromyces lactisMutation(s): 0 
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
EL18S [auth Q]186Kluyveromyces lactisMutation(s): 0 
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Entity ID: 20
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EL19T [auth R]189Kluyveromyces lactisMutation(s): 0 
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
EL20U [auth S]172Kluyveromyces lactisMutation(s): 0 
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetailsImage
EL21V [auth T]160Kluyveromyces lactisMutation(s): 0 
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetailsImage
EL22W [auth U]121Kluyveromyces lactisMutation(s): 0 
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetailsImage
UL14X [auth V]137Kluyveromyces lactisMutation(s): 0 
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetailsImage
EL24Y [auth W]155Kluyveromyces lactisMutation(s): 0 
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetailsImage
UL23Z [auth X]142Kluyveromyces lactisMutation(s): 0 
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetailsImage
UL24AA [auth Y]127Kluyveromyces lactisMutation(s): 0 
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetailsImage
EL27BA [auth Z]136Kluyveromyces lactisMutation(s): 0 
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Entity ID: 29
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UL15CA [auth a]149Kluyveromyces lactisMutation(s): 0 
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetailsImage
EL29DA [auth b]59Kluyveromyces lactisMutation(s): 0 
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetailsImage
EL30EA [auth c]105Kluyveromyces lactisMutation(s): 0 
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetailsImage
EL31FA [auth d]113Kluyveromyces lactisMutation(s): 0 
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetailsImage
EL32GA [auth e]130Kluyveromyces lactisMutation(s): 0 
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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetailsImage
EL33HA [auth f]107Kluyveromyces lactisMutation(s): 0 
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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetailsImage
EL34IA [auth g]121Kluyveromyces lactisMutation(s): 0 
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Entity ID: 36
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UL29JA [auth h]120Kluyveromyces lactisMutation(s): 0 
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Entity ID: 37
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EL36KA [auth i]100Kluyveromyces lactisMutation(s): 0 
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Entity ID: 38
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EL37LA [auth j]88Kluyveromyces lactisMutation(s): 0 
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Entity ID: 39
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EL38MA [auth k]78Kluyveromyces lactisMutation(s): 0 
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Entity ID: 40
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EL39NA [auth l]51Kluyveromyces lactisMutation(s): 0 
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Entity ID: 41
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EL40OA [auth m]128Kluyveromyces lactisMutation(s): 0 
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Entity ID: 42
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EL41PA [auth n]25Kluyveromyces lactisMutation(s): 0 
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Entity ID: 43
MoleculeChainsSequence LengthOrganismDetailsImage
EL42QA [auth o]106Kluyveromyces lactisMutation(s): 0 
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Entity ID: 44
MoleculeChainsSequence LengthOrganismDetailsImage
EL43RA [auth p]92Kluyveromyces lactisMutation(s): 0 
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Entity ID: 45
MoleculeChainsSequence LengthOrganismDetailsImage
UL1SA [auth t]217Kluyveromyces lactisMutation(s): 0 
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Entity ID: 1
MoleculeChainsLengthOrganismImage
25S RRNAA [auth 1]3397Kluyveromyces lactis
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Entity ID: 2
MoleculeChainsLengthOrganismImage
5S RRNAB [auth 3]121Kluyveromyces lactis
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Entity ID: 3
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5.8S RRNAC [auth 4]158Kluyveromyces lactis
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