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 1.4 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: https://doi.org/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 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
MoleculeChains Sequence LengthOrganismDetailsImage
Peptide chain release factor 2F [auth Z]365Escherichia coliMutation(s): 0 
Gene Names: prfB/SupK
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S2G [auth E]256Escherichia coliMutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S3H [auth F]239Escherichia coliMutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S4I [auth G]209Escherichia coliMutation(s): 0 
UniProt
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S5J [auth H]162Escherichia coliMutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S6K [auth I]101Escherichia coliMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S7L [auth J]156Escherichia coliMutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S8M [auth K]138Escherichia coliMutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S9N [auth L]128Escherichia coliMutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S10O [auth M]105Escherichia coliMutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S11P [auth N]129Escherichia coliMutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S12Q [auth O]135Escherichia coliMutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S13R [auth P]126Escherichia coliMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S14S [auth Q]61Escherichia coliMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S15T [auth R]89Escherichia coliMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S16U [auth S]91Escherichia coliMutation(s): 0 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S17V [auth T]105Escherichia coliMutation(s): 0 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S18W [auth U]88Escherichia coliMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S19X [auth V]93Escherichia coliMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S20Y [auth W]106Escherichia coliMutation(s): 0 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN THXZ [auth X]26Escherichia coliMutation(s): 0 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L1AA [auth c]228Escherichia coliMutation(s): 0 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L2BA [auth d]178Escherichia coliMutation(s): 0 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L3CA [auth e]338Escherichia coliMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L4DA [auth f]246Escherichia coliMutation(s): 0 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L5EA [auth g]176Escherichia coliMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L6FA [auth h]177Escherichia coliMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L11GA [auth l]141Escherichia coliMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L13HA [auth m]145Escherichia coliMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L14IA [auth n]122Escherichia coliMutation(s): 0 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L15JA [auth o]164Escherichia coliMutation(s): 0 
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50S RIBOSOMAL PROTEIN L16KA [auth p]138Escherichia coliMutation(s): 0 
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50S RIBOSOMAL PROTEIN L18LA [auth q]186Escherichia coliMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L19MA [auth r]66Escherichia coliMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L22NA [auth s]113Escherichia coliMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L23OA [auth t]84Escherichia coliMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L24PA [auth u]119Escherichia coliMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L25QA [auth v]94Escherichia coliMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L29RA [auth w]70Escherichia coliMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L30SA [auth x]60Escherichia coliMutation(s): 0 
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MoleculeChains LengthOrganismImage
30S 16S RIBOSOMAL RNA1,522Escherichia coli
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T-RNA(PHE)76Escherichia coli
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MoleculeChains LengthOrganismImage
A- AND P-SITE MESSENGER RNA CODONS6Escherichia coli
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50S 23S RIBOSOMAL RNAD [auth a]2,916Escherichia coli
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Entity ID: 5
MoleculeChains LengthOrganismImage
50S 5S RIBOSOMAL RNAE [auth b]123Escherichia coli
Sequence Annotations
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  • Reference Sequence
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  (Full details and data files)

  • 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
  • Version 1.4: 2024-02-14
    Changes: Data collection, Database references, Refinement description