1ML5

Structure of the E. coli ribosomal termination complex with release factor 2


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 14.0 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

Structure of the Escherichia coli ribosomal termination complex with release factor 2

Klaholz, B.P.Pape, T.Zavialov, A.V.Myasnikov, A.G.Orlova, E.V.Vestergaard, B.Ehrenberg, M.van Heel, M.

(2003) Nature 421: 90-94

  • DOI: 10.1038/nature01225
  • Primary Citation of Related Structures:  
    1ML5

  • PubMed Abstract: 
  • Termination of protein synthesis occurs when the messenger RNA presents a stop codon in the ribosomal aminoacyl (A) site. Class I release factor proteins (RF1 or RF2) are believed to recognize stop codons via tripeptide motifs, leading to release of ...

    Termination of protein synthesis occurs when the messenger RNA presents a stop codon in the ribosomal aminoacyl (A) site. Class I release factor proteins (RF1 or RF2) are believed to recognize stop codons via tripeptide motifs, leading to release of the completed polypeptide chain from its covalent attachment to transfer RNA in the ribosomal peptidyl (P) site. Class I RFs possess a conserved GGQ amino-acid motif that is thought to be involved directly in protein-transfer-RNA bond hydrolysis. Crystal structures of bacterial and eukaryotic class I RFs have been determined, but the mechanism of stop codon recognition and peptidyl-tRNA hydrolysis remains unclear. Here we present the structure of the Escherichia coli ribosome in a post-termination complex with RF2, obtained by single-particle cryo-electron microscopy (cryo-EM). Fitting the known 70S and RF2 structures into the electron density map reveals that RF2 adopts a different conformation on the ribosome when compared with the crystal structure of the isolated protein. The amino-terminal helical domain of RF2 contacts the factor-binding site of the ribosome, the 'SPF' loop of the protein is situated close to the mRNA, and the GGQ-containing domain of RF2 interacts with the peptidyl-transferase centre (PTC). By connecting the ribosomal decoding centre with the PTC, RF2 functionally mimics a tRNA molecule in the A site. Translational termination in eukaryotes is likely to be based on a similar mechanism.


    Organizational Affiliation

    Department of Biological Sciences, Imperial College of Science, Technology and Medicine, London SW7 2AY, UK.



Macromolecules

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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Peptide chain release factor 2Z365Escherichia coliMutation(s): 0 
Gene Names: prfB/SupK
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Entity ID: 7
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30S RIBOSOMAL PROTEIN S2E256Escherichia coliMutation(s): 0 
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Entity ID: 8
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30S RIBOSOMAL PROTEIN S3F239Escherichia coliMutation(s): 0 
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Entity ID: 9
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30S RIBOSOMAL PROTEIN S4G209Escherichia coliMutation(s): 0 
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Entity ID: 10
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30S RIBOSOMAL PROTEIN S5H162Escherichia coliMutation(s): 0 
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Entity ID: 11
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30S RIBOSOMAL PROTEIN S6I101Escherichia coliMutation(s): 0 
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Entity ID: 12
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30S RIBOSOMAL PROTEIN S7J156Escherichia coliMutation(s): 0 
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30S RIBOSOMAL PROTEIN S8K138Escherichia coliMutation(s): 0 
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Entity ID: 14
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30S RIBOSOMAL PROTEIN S9L128Escherichia coliMutation(s): 0 
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Entity ID: 15
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30S RIBOSOMAL PROTEIN S10M105Escherichia coliMutation(s): 0 
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Entity ID: 16
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30S RIBOSOMAL PROTEIN S11N129Escherichia coliMutation(s): 0 
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30S RIBOSOMAL PROTEIN S12O135Escherichia coliMutation(s): 0 
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Entity ID: 18
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30S RIBOSOMAL PROTEIN S13P126Escherichia coliMutation(s): 0 
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Entity ID: 19
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30S RIBOSOMAL PROTEIN S14Q61Escherichia coliMutation(s): 0 
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Entity ID: 20
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30S RIBOSOMAL PROTEIN S15R89Escherichia coliMutation(s): 0 
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30S RIBOSOMAL PROTEIN S16S91Escherichia coliMutation(s): 0 
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30S RIBOSOMAL PROTEIN S17T105Escherichia coliMutation(s): 0 
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30S RIBOSOMAL PROTEIN S18U88Escherichia coliMutation(s): 0 
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30S RIBOSOMAL PROTEIN S19V93Escherichia coliMutation(s): 0 
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30S RIBOSOMAL PROTEIN S20W106Escherichia coliMutation(s): 0 
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Entity ID: 26
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30S RIBOSOMAL PROTEIN THXX26Escherichia coliMutation(s): 0 
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Entity ID: 27
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50S RIBOSOMAL PROTEIN L1c228Escherichia coliMutation(s): 0 
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50S RIBOSOMAL PROTEIN L2d178Escherichia coliMutation(s): 0 
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50S RIBOSOMAL PROTEIN L3e338Escherichia coliMutation(s): 0 
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50S RIBOSOMAL PROTEIN L4f246Escherichia coliMutation(s): 0 
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Entity ID: 31
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50S RIBOSOMAL PROTEIN L5g176Escherichia coliMutation(s): 0 
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50S RIBOSOMAL PROTEIN L6h177Escherichia coliMutation(s): 0 
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Entity ID: 33
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50S RIBOSOMAL PROTEIN L11l141Escherichia coliMutation(s): 0 
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Entity ID: 34
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50S RIBOSOMAL PROTEIN L13m145Escherichia coliMutation(s): 0 
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50S RIBOSOMAL PROTEIN L14n122Escherichia coliMutation(s): 0 
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50S RIBOSOMAL PROTEIN L15o164Escherichia coliMutation(s): 0 
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50S RIBOSOMAL PROTEIN L16p138Escherichia coliMutation(s): 0 
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50S RIBOSOMAL PROTEIN L18q186Escherichia coliMutation(s): 0 
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50S RIBOSOMAL PROTEIN L19r66Escherichia coliMutation(s): 0 
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50S RIBOSOMAL PROTEIN L22s113Escherichia coliMutation(s): 0 
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50S RIBOSOMAL PROTEIN L23t84Escherichia coliMutation(s): 0 
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50S RIBOSOMAL PROTEIN L24u119Escherichia coliMutation(s): 0 
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50S RIBOSOMAL PROTEIN L25v94Escherichia coliMutation(s): 0 
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50S RIBOSOMAL PROTEIN L29w70Escherichia coliMutation(s): 0 
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50S RIBOSOMAL PROTEIN L30x60Escherichia coliMutation(s): 0 
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30S 16S RIBOSOMAL RNAA1522Escherichia coli
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T-RNA(PHE)B76Escherichia coli
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  • Entity ID: 3
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    A- AND P-SITE MESSENGER RNA CODONSC6Escherichia coli
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    50S 23S RIBOSOMAL RNAa2916Escherichia coli
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    Entity ID: 5
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    50S 5S RIBOSOMAL RNAb123Escherichia coli
    Experimental Data & Validation

    Experimental Data

    • Method: ELECTRON MICROSCOPY
    • Resolution: 14.0 Å
    • Aggregation State: PARTICLE 
    • Reconstruction Method: SINGLE PARTICLE 

    Structure Validation

    View Full Validation Report



    Entry History 

    Deposition Data

    Revision History 

    • Version 1.0: 2003-01-14
      Type: Initial release
    • Version 1.1: 2008-04-28
      Changes: Version format compliance
    • Version 1.2: 2011-07-13
      Changes: Non-polymer description, Version format compliance
    • Version 1.3: 2019-12-18
      Changes: Advisory, Derived calculations, Other