5JUT

Saccharomyces cerevisiae 80S ribosome bound with elongation factor eEF2-GDP-sordarin and Taura Syndrome Virus IRES, Structure IV (almost non-rotated 40S subunit)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.00 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

Ensemble cryo-EM uncovers inchworm-like translocation of a viral IRES through the ribosome.

Abeyrathne, P.D.Koh, C.S.Grant, T.Grigorieff, N.Korostelev, A.A.

(2016) Elife 5

  • DOI: 10.7554/eLife.14874
  • Primary Citation of Related Structures:  
    5JUP, 5JUS, 5JUU, 5JUT, 5JUO

  • PubMed Abstract: 
  • Internal ribosome entry sites (IRESs) mediate cap-independent translation of viral mRNAs. Using electron cryo-microscopy of a single specimen, we present five ribosome structures formed with the Taura syndrome virus IRES and translocase eEF2•GTP boun ...

    Internal ribosome entry sites (IRESs) mediate cap-independent translation of viral mRNAs. Using electron cryo-microscopy of a single specimen, we present five ribosome structures formed with the Taura syndrome virus IRES and translocase eEF2•GTP bound with sordarin. The structures suggest a trajectory of IRES translocation, required for translation initiation, and provide an unprecedented view of eEF2 dynamics. The IRES rearranges from extended to bent to extended conformations. This inchworm-like movement is coupled with ribosomal inter-subunit rotation and 40S head swivel. eEF2, attached to the 60S subunit, slides along the rotating 40S subunit to enter the A site. Its diphthamide-bearing tip at domain IV separates the tRNA-mRNA-like pseudoknot I (PKI) of the IRES from the decoding center. This unlocks 40S domains, facilitating head swivel and biasing IRES translocation via hitherto-elusive intermediates with PKI captured between the A and P sites. The structures suggest missing links in our understanding of tRNA translocation.


    Organizational Affiliation

    RNA Therapeutics Institute, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, United States.



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eS10 (yeast S10)HB105Saccharomyces cerevisiaeMutation(s): 0 
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uS17 (yeast S11)IB156Saccharomyces cerevisiaeMutation(s): 0 
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eS12 (yeast S12)JB143Saccharomyces cerevisiaeMutation(s): 0 
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uS15 (yeast S13)KB151Saccharomyces cerevisiaeMutation(s): 0 
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uS11 (yeast S14)LB137Saccharomyces cerevisiaeMutation(s): 0 
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uS19 (yeast S15)MB142Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 66
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uS9 (yeast S16)NB143Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 67
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eS17 (yeast S17)OB136Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P02407 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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uS13 (yeast S18)PB146Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 69
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eS19 (yeast S19)QB144Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 70
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uS10 (yeast S20)RB121Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 71
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eS21 (yeast S21)SB87Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 72
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uS8 (yeast S22)TB130Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 73
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uS12 (yeast S23)UB145Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 74
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eS24 (yeast S24)VB135Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 75
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eS25 (yeast S25)WB108Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for Q3E792 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 76
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eS26 (yeast S26)XB119Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 77
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eS27 (yeast S27)YB82Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 78
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eS28 (yeast S28)ZB67Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 79
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uS14 (yeast S29)AC56Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 80
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eS30 (yeast S30)BC63Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 81
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eS31 (yeast S31)CC152Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 82
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yeast eEF2DC842Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 1
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18S ribosomal RNAA1798Saccharomyces cerevisiae
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Entity ID: 2
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25S ribosomal RNAB3396Saccharomyces cerevisiae
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Entity ID: 3
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5.8S ribosomal RNAC158Saccharomyces cerevisiae
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Entity ID: 4
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5S ribosomal RNAD121Saccharomyces cerevisiae
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Entity ID: 83
MoleculeChainsLengthOrganismImage
IRESEC201Taura syndrome virus
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO1
Query on SO1

Download CCD File 
DC
[1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID
C27 H42 O8
DIBGPTPYRVEPSP-OHFCZZTFSA-N
 Ligand Interaction
GDP
Query on GDP

Download CCD File 
DC
GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
 Ligand Interaction
MG
Query on MG

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DC
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
DDE
Query on DDE
DCL-PEPTIDE LINKINGC13 H24 N5 O3HIS
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.00 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 StatesGM62580
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM106105
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM107465
Howard Hughes Medical Institute (HHMI)United States--

Revision History 

  • Version 1.0: 2016-10-05
    Type: Initial release
  • Version 1.1: 2017-09-13
    Changes: Author supporting evidence, Data collection
  • Version 1.2: 2019-11-20
    Changes: Author supporting evidence
  • Version 1.3: 2019-11-27
    Changes: Author supporting evidence