6WOO

CryoEM structure of yeast 80S ribosome with Met-tRNAiMet, eIF5B, and GDP


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report



Literature

An active role of the eukaryotic large ribosomal subunit in translation initiation fidelity.

Wang, J.Wang, J.Puglisi, J.Fernandez, I.S.

To be published.

Macromolecules

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uL2A249Saccharomyces cerevisiaeMutation(s): 0 
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uL3B384Saccharomyces cerevisiaeMutation(s): 0 
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uL4C359Saccharomyces cerevisiaeMutation(s): 0 
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uL18D295Saccharomyces cerevisiaeMutation(s): 0 
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eL6E175Saccharomyces cerevisiaeMutation(s): 0 
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uL30F222Saccharomyces cerevisiaeMutation(s): 0 
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eL8G233Saccharomyces cerevisiaeMutation(s): 0 
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uL16I216Saccharomyces cerevisiaeMutation(s): 0 
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uL5J168Saccharomyces cerevisiaeMutation(s): 0 
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eL13L198Saccharomyces cerevisiaeMutation(s): 0 
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eL14M136Saccharomyces cerevisiaeMutation(s): 0 
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eL15N202Saccharomyces cerevisiaeMutation(s): 0 
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eL19R188Saccharomyces cerevisiaeMutation(s): 0 
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eL22U100Saccharomyces cerevisiaeMutation(s): 0 
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uL14V132Saccharomyces cerevisiaeMutation(s): 0 
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eL24W62Saccharomyces cerevisiaeMutation(s): 0 
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uL24Y125Saccharomyces cerevisiaeMutation(s): 0 
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eL27Z134Saccharomyces cerevisiaeMutation(s): 0 
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uL15a147Saccharomyces cerevisiaeMutation(s): 0 
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eL29b57Saccharomyces cerevisiaeMutation(s): 0 
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eL30c97Saccharomyces cerevisiaeMutation(s): 0 
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eL31d106Saccharomyces cerevisiaeMutation(s): 0 
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eL32e122Saccharomyces cerevisiaeMutation(s): 0 
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eL33f105Saccharomyces cerevisiaeMutation(s): 0 
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eL34g121Saccharomyces cerevisiaeMutation(s): 0 
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uL29h116Saccharomyces cerevisiaeMutation(s): 0 
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eL36i98Saccharomyces cerevisiaeMutation(s): 0 
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eL38k76Saccharomyces cerevisiaeMutation(s): 0 
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eL40m51Saccharomyces cerevisiaeMutation(s): 0 
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eL41n23Saccharomyces cerevisiaeMutation(s): 0 
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eL42o101Saccharomyces cerevisiaeMutation(s): 0 
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eL43p87Saccharomyces cerevisiaeMutation(s): 0 
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uL1q217Saccharomyces cerevisiaeMutation(s): 0 
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uL10r195Saccharomyces cerevisiaeMutation(s): 0 
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L10K152Saccharomyces cerevisiaeMutation(s): 0 
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uS2AA206Saccharomyces cerevisiaeMutation(s): 0 
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eS1BB214Saccharomyces cerevisiaeMutation(s): 0 
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uS5CC217Saccharomyces cerevisiaeMutation(s): 0 
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uS3DD223Saccharomyces cerevisiaeMutation(s): 0 
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eS4EE257Saccharomyces cerevisiaeMutation(s): 0 
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uS7FF206Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: RPS5GI526_G0003357PACBIOSEQ_LOCUS2208PACBIOSEQ_LOCUS3487PACBIOSEQ_LOCUS3669PACBIOSEQ_LOCUS3731PACBIOSEQ_LOCUS3784PACBIOSEQ_LOCUS3808PACBIOSEQ_LOCUS3826
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eS6GG226Saccharomyces cerevisiaeMutation(s): 0 
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eS7HH184Saccharomyces cerevisiaeMutation(s): 0 
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eS8II199Saccharomyces cerevisiaeMutation(s): 0 
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uS4JJ182Saccharomyces cerevisiaeMutation(s): 0 
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eS10KK96Saccharomyces cerevisiaeMutation(s): 0 
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uS17LL145Saccharomyces cerevisiaeMutation(s): 0 
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eS12MM124Saccharomyces cerevisiaeMutation(s): 0 
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uS15NN150Saccharomyces cerevisiaeMutation(s): 0 
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uS11OO127Saccharomyces cerevisiaeMutation(s): 0 
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uS19PP103Saccharomyces cerevisiaeMutation(s): 0 
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uS19QQ141Saccharomyces cerevisiaeMutation(s): 0 
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eS17RR123Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 66
MoleculeChainsSequence LengthOrganismDetailsImage
uS13SS136Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 67
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eS19TT143Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 68
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uS10UU106Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 69
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eS21VV87Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 70
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uS8WW129Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 71
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uS12XX144Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 72
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eS24YY134Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 73
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eS25ZZ70Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 74
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eS26aa97Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 75
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eS27bb81Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 76
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eS28cc63Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 77
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uS14dd53Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 78
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eS30ee53Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 79
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eS31ff57Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 80
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RACK1gg318Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 82
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eIF5B1600Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: FUN12YAL035W
EC: 3.6.5.3
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Entity ID: 1
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25S ribosomal RNA53271Saccharomyces cerevisiae
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Entity ID: 2
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5S ribosomal RNA7121Saccharomyces cerevisiae
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Entity ID: 3
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5.8S ribosomal rRNA8157Saccharomyces cerevisiae
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Entity ID: 81
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18S ribosomal RNA21796Saccharomyces cerevisiae
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Entity ID: 83
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Met-tRNA-iMet376Saccharomyces cerevisiae
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  • Entity ID: 84
    MoleculeChainsLengthOrganismImage
    mRNA46Saccharomyces cerevisiae
    Small Molecules
    Ligands 4 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    GDP
    Query on GDP

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    1
    GUANOSINE-5'-DIPHOSPHATE
    C10 H15 N5 O11 P2
    QGWNDRXFNXRZMB-UUOKFMHZSA-N
     Ligand Interaction
    U6A
    Query on U6A

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    3
    N-carboxy-L-threonine
    C5 H9 N O5
    OJLPTWSLDBSLEH-GBXIJSLDSA-N
     Ligand Interaction
    MET
    Query on MET

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    3
    METHIONINE
    C5 H11 N O2 S
    FFEARJCKVFRZRR-BYPYZUCNSA-N
     Ligand Interaction
    ZN
    Query on ZN

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    aa, bb, ff, j, m, o
    ZINC ION
    Zn
    PTFCDOFLOPIGGS-UHFFFAOYSA-N
     Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: ELECTRON MICROSCOPY
    • Resolution: 2.90 Å
    • Aggregation State: PARTICLE 
    • Reconstruction Method: SINGLE PARTICLE 

    Structure Validation

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    Entry History 

    Deposition Data

    Revision History 

    • Version 1.0: 2020-09-23
      Type: Initial release