4V4B

Structure of the ribosomal 80S-eEF2-sordarin complex from yeast obtained by docking atomic models for RNA and protein components into a 11.7 A cryo-EM map.


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 11.7 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

Domain movements of elongation factor eEF2 and the eukaryotic 80S ribosome facilitate tRNA translocation.

Spahn, C.M.Gomez-Lorenzo, M.G.Grassucci, R.A.Jorgensen, R.Andersen, G.R.Beckmann, R.Penczek, P.A.Ballesta, J.P.Frank, J.

(2004) EMBO J 23: 1008-1019

  • DOI: 10.1038/sj.emboj.7600102
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • An 11.7-A-resolution cryo-EM map of the yeast 80S.eEF2 complex in the presence of the antibiotic sordarin was interpreted in molecular terms, revealing large conformational changes within eEF2 and the 80S ribosome, including a rearrangement of the fu ...

    An 11.7-A-resolution cryo-EM map of the yeast 80S.eEF2 complex in the presence of the antibiotic sordarin was interpreted in molecular terms, revealing large conformational changes within eEF2 and the 80S ribosome, including a rearrangement of the functionally important ribosomal intersubunit bridges. Sordarin positions domain III of eEF2 so that it can interact with the sarcin-ricin loop of 25S rRNA and protein rpS23 (S12p). This particular conformation explains the inhibitory action of sordarin and suggests that eEF2 is stalled on the 80S ribosome in a conformation that has similarities with the GTPase activation state. A ratchet-like subunit rearrangement (RSR) occurs in the 80S.eEF2.sordarin complex that, in contrast to Escherichia coli 70S ribosomes, is also present in vacant 80S ribosomes. A model is suggested, according to which the RSR is part of a mechanism for moving the tRNAs during the translocation reaction.


    Related Citations: 
    • EF-G-dependent GTP hydrolysis induces translocation accompanied by large conformational changes in the 70S ribosome
      Agrawal, R.K., Heagle, A.B., Penczek, P., Grassucci, R.A., Frank, J.
      (1999) Nat Struct Biol 6: 643
    • The large ribosomal subunit stalk as a regulatory element of the eukaryotic translational machinery.
      Ballesta, J.P., Remacha, M.
      (1996) Prog Nucleic Acid Res Mol Biol 55: 157
    • The complete atomic structure of the large ribosomal subunit at 2.4 A resolution
      Ban, N., Nissen, P., Hansen, J., Moore, P.B., Steitz, T.A.
      (2000) Science 289: 905

    Organizational Affiliation

    Wadsworth Center, Health Research Inc., Howard Hughes Medical Institute, Albany, NY 12201-0509, USA. christian.spahn@charite.de



Macromolecules

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S0-AAB185Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S3AC192Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S9-AAD179Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S22AH129Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S20AJ100Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S23AL118Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S13AO65Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S11AQ76Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L1BA217Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L2BB253Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L3BC386Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L8-ABG119Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L9-ABH191Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L11BJ173Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L12BK131Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L15-ABL203Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L16-ABM146Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L17-ABN183Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L18BO120Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L21-ABQ100Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L23BR137Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 39
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L25BT83Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L28BV148Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L32B0130Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 43
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L31BW112Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 45
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L37-ABY87Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 46
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L42BZ105Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S14-AAK136Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S18AM132Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S29-BAN36Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S15AS80Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Elongation factor 2AT842Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L4-BBD361Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L5BE222Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L7-ABF162Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L10BI168Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L19BP142Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L24-ABS56Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L26-ABU126Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 44
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L35BX120Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 47
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L43B991Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S2AE149Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S5AG150Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S16AI142Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 18
MoleculeChainsLengthOrganism
5.8S/25S ribosomal RNAB32999Saccharomyces cerevisiae

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Entity ID: 19
MoleculeChainsLengthOrganism
5S RIBOSOMAL RNAB4125Saccharomyces cerevisiae

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Entity ID: 1
MoleculeChainsLengthOrganism
18S ribosomal RNAAA1507Saccharomyces cerevisiae
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 11.7 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: 2015-03-18
    Changes: Other
  • Version 1.3: 2019-12-18
    Changes: Data collection, Database references, Other