4V8Z

Cryo-EM reconstruction of the 80S-eIF5B-Met-itRNAMet Eukaryotic Translation Initiation Complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 6.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report



Literature

Molecular architecture of a eukaryotic translational initiation complex.

Fernandez, I.S.Bai, X.C.Hussain, T.Kelley, A.C.Lorsch, J.R.Ramakrishnan, V.Scheres, S.H.W.

(2013) Science 342: 1240585-1240585

  • DOI: 10.1126/science.1240585
  • Primary Citation of Related Structures:  
    4V8Y, 4V8Z

  • PubMed Abstract: 
  • The last step in eukaryotic translational initiation involves the joining of the large and small subunits of the ribosome, with initiator transfer RNA (Met-tRNA(i)(Met)) positioned over the start codon of messenger RNA in the P site. This step is catalyz ...

    The last step in eukaryotic translational initiation involves the joining of the large and small subunits of the ribosome, with initiator transfer RNA (Met-tRNA(i)(Met)) positioned over the start codon of messenger RNA in the P site. This step is catalyzed by initiation factor eIF5B. We used recent advances in cryo-electron microscopy (cryo-EM) to determine a structure of the eIF5B initiation complex to 6.6 angstrom resolution from <3% of the population, comprising just 5143 particles. The structure reveals conformational changes in eIF5B, initiator tRNA, and the ribosome that provide insights into the role of eIF5B in translational initiation. The relatively high resolution obtained from such a small fraction of a heterogeneous sample suggests a general approach for characterizing the structure of other dynamic or transient biological complexes.


    Organizational Affiliation

    MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, CB2 0QH, United Kingdom.



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40S RIBOSOMAL PROTEIN S27-A A182Saccharomyces cerevisiaeMutation(s): 0 
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40S RIBOSOMAL PROTEIN S28-A A267Saccharomyces cerevisiaeMutation(s): 0 
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40S RIBOSOMAL PROTEIN S30-A A463Saccharomyces cerevisiaeMutation(s): 0 
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UBIQUITIN-40S RIBOSOMAL PROTEIN S31 A5152Saccharomyces cerevisiaeMutation(s): 0 
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GUANINE NUCLEOTIDE-BINDING PROTEIN SUBUNIT BETA-LIKE PROTEIN A6319Saccharomyces cerevisiaeMutation(s): 0 
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40S RIBOSOMAL PROTEIN S21-A AV87Saccharomyces cerevisiaeMutation(s): 0 
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40S RIBOSOMAL PROTEIN S22-A AW130Saccharomyces cerevisiaeMutation(s): 0 
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40S RIBOSOMAL PROTEIN S24-A AY135Saccharomyces cerevisiaeMutation(s): 0 
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60S RIBOSOMAL PROTEIN L3 BB386Saccharomyces cerevisiaeMutation(s): 0 
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60S RIBOSOMAL PROTEIN L5 BD296Saccharomyces cerevisiaeMutation(s): 0 
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60S RIBOSOMAL PROTEIN L8-A BG255Saccharomyces cerevisiaeMutation(s): 0 
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60S RIBOSOMAL PROTEIN L9-A BH191Saccharomyces cerevisiaeMutation(s): 0 
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60S RIBOSOMAL PROTEIN L10 BI220Saccharomyces cerevisiaeMutation(s): 0 
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60S RIBOSOMAL PROTEIN L11-A BJ173Saccharomyces cerevisiaeMutation(s): 0 
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60S RIBOSOMAL PROTEIN L16-A BO198Saccharomyces cerevisiaeMutation(s): 20 
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60S RIBOSOMAL PROTEIN L18-A BQ185Saccharomyces cerevisiaeMutation(s): 0 
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60S RIBOSOMAL PROTEIN L19-B BR188Saccharomyces cerevisiaeMutation(s): 0 
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60S RIBOSOMAL PROTEIN L20-B BS172Saccharomyces cerevisiaeMutation(s): 0 
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60S RIBOSOMAL PROTEIN L21-A BT159Saccharomyces cerevisiaeMutation(s): 0 
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60S RIBOSOMAL PROTEIN L22-A BU120Saccharomyces cerevisiaeMutation(s): 0 
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60S RIBOSOMAL PROTEIN L23-A BV136Saccharomyces cerevisiaeMutation(s): 0 
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60S RIBOSOMAL PROTEIN L24-A BW155Saccharomyces cerevisiaeMutation(s): 0 
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60S RIBOSOMAL PROTEIN L25 BX141Saccharomyces cerevisiaeMutation(s): 0 
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60S RIBOSOMAL PROTEIN L26-A BY126Saccharomyces cerevisiaeMutation(s): 0 
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60S RIBOSOMAL PROTEIN L27-A BZ135Saccharomyces cerevisiaeMutation(s): 0 
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60S RIBOSOMAL PROTEIN L28 Ba148Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 62
MoleculeChainsSequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN L29 Bb58Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 63
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60S RIBOSOMAL PROTEIN L30 Bc104Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 64
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60S RIBOSOMAL PROTEIN L31-A Bd112Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 65
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60S RIBOSOMAL PROTEIN L32 Be129Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P38061 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 66
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60S RIBOSOMAL PROTEIN L33-A Bf106Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 67
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60S RIBOSOMAL PROTEIN L34-A Bg120Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P87262 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 68
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60S RIBOSOMAL PROTEIN L35-B Bh119Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 69
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60S RIBOSOMAL PROTEIN L36-A Bi99Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 70
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60S RIBOSOMAL PROTEIN L37-A Bj87Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 71
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60S RIBOSOMAL PROTEIN L38 Bk77Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 72
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60S RIBOSOMAL PROTEIN L39 Bl50Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 73
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UBIQUITIN-60S RIBOSOMAL PROTEIN L40 Bm128Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 74
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60S RIBOSOMAL PROTEIN L41-B Bn25Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 75
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60S RIBOSOMAL PROTEIN L42-A Bo105Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 76
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60S ACIDIC RIBOSOMAL PROTEIN P0 Bq312Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 77
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60S ACIDIC RIBOSOMAL PROTEIN P1 Br47Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 78
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60S ACIDIC RIBOSOMAL PROTEIN P2 Bs46Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 83
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EUKARYOTIC TRANSLATION INITIATION FACTOR 5B, PROBABLE TRANSLATION INITIATION FACTOR IF-2 CV586Saccharomyces cerevisiaeMethanothermobacter thermautotrophicus
This entity is chimeric
Mutation(s): 0 
EC: 3.6.5.3
Find proteins for P39730 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Find proteins for O26359 (Methanothermobacter thermautotrophicus (strain ATCC 29096 / DSM 1053 / JCM 10044 / NBRC 100330 / Delta H))
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Entity ID: 79
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18S RIBOSOMAL RNAB21800Saccharomyces cerevisiae
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Entity ID: 80
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25S RIBOSOMAL RNAB53396Saccharomyces cerevisiae
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Entity ID: 81
MoleculeChainsLengthOrganismImage
5S RIBOSOMAL RNAB7121Saccharomyces cerevisiae
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Entity ID: 82
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5.8S RIBOSOMAL RNAB8158Saccharomyces cerevisiae
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Entity ID: 84
MoleculeChainsLengthOrganismImage
EUKARYOTIC RIBOSOMAL PI TRNACW76Saccharomyces cerevisiae
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  • Entity ID: 85
    MoleculeChainsLengthOrganismImage
    5'-R(*AP*UP*GP)-3'CX3Saccharomyces cerevisiae
    Small Molecules
    Ligands 4 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    GCP
    Query on GCP

    Download Ideal Coordinates CCD File 
    CV
    PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER
    C11 H18 N5 O13 P3
    PHBDHXOBFUBCJD-KQYNXXCUSA-N
     Ligand Interaction
    OHX
    Query on OHX

    Download Ideal Coordinates CCD File 
    A3, A6, AC, AI, AL, AN, AP, B2, B5, B7, BR, Bn, CV, CX
    osmium (III) hexammine
    H12 N6 Os
    OWCQTVJQFLTQTE-UHFFFAOYSA-N
     Ligand Interaction
    ZN
    Query on ZN

    Download Ideal Coordinates CCD File 
    A0, A1, A3, A5, Bj, Bm
    ZINC ION
    Zn
    PTFCDOFLOPIGGS-UHFFFAOYSA-N
     Ligand Interaction
    MG
    Query on MG

    Download Ideal Coordinates CCD File 
    A0, A3, A5, AB, AC, AE, AG, AI, AJ, AL, AN, AP, AS, AU, B2, B5, B7, BD, BF, BS, CW
    MAGNESIUM ION
    Mg
    JLVVSXFLKOJNIY-UHFFFAOYSA-N
     Ligand Interaction
    Modified Residues  1 Unique
    IDChainsTypeFormula2D DiagramParent
    HSO
    Query on HSO
    CVL-PEPTIDE LINKINGC6 H12 N3 OHIS
    Experimental Data & Validation

    Experimental Data

    • Method: ELECTRON MICROSCOPY
    • Resolution: 6.60 Å
    • Aggregation State: PARTICLE 
    • Reconstruction Method: SINGLE PARTICLE 

    Structure Validation

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    Entry History 

    Deposition Data

    Revision History 

    • 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 3.0: 2018-04-18
      Changes: Atomic model, Data collection, Database references, Other, Structure summary
    • Version 3.1: 2019-08-21
      Changes: Data collection, Database references, Derived calculations
    • Version 3.2: 2019-10-09
      Changes: Data collection, Source and taxonomy, Structure summary
    • Version 3.3: 2019-10-23
      Changes: Data collection, Database references
    • Version 4.0: 2019-12-11
      Changes: Other, Polymer sequence