5MGP

Structural basis for ArfA-RF2 mediated translation termination on stop-codon lacking mRNAs


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural basis for ArfA-RF2-mediated translation termination on mRNAs lacking stop codons.

Huter, P.Muller, C.Beckert, B.Arenz, S.Berninghausen, O.Beckmann, R.Wilson, D.N.

(2017) Nature 541: 546-549

  • DOI: https://doi.org/10.1038/nature20821
  • Primary Citation of Related Structures:  
    5MGP

  • PubMed Abstract: 

    In bacteria, ribosomes stalled on truncated mRNAs that lack a stop codon are rescued by the transfer-messenger RNA (tmRNA), alternative rescue factor A (ArfA) or ArfB systems. Although tmRNA-ribosome and ArfB-ribosome structures have been determined, how ArfA recognizes the presence of truncated mRNAs and recruits the canonical termination release factor RF2 to rescue the stalled ribosomes is unclear. Here we present a cryo-electron microscopy reconstruction of the Escherichia coli 70S ribosome stalled on a truncated mRNA in the presence of ArfA and RF2. The structure shows that the C terminus of ArfA binds within the mRNA entry channel on the small ribosomal subunit, and explains how ArfA distinguishes between ribosomes that bear truncated or full-length mRNAs. The N terminus of ArfA establishes several interactions with the decoding domain of RF2, and this finding illustrates how ArfA recruits RF2 to the stalled ribosome. Furthermore, ArfA is shown to stabilize a unique conformation of the switch loop of RF2, which mimics the canonical translation termination state by directing the catalytically important GGQ motif within domain 3 of RF2 towards the peptidyl-transferase centre of the ribosome. Thus, our structure reveals not only how ArfA recruits RF2 to the ribosome but also how it promotes an active conformation of RF2 to enable translation termination in the absence of a stop codon.


  • Organizational Affiliation

    Gene Center, Department of Biochemistry and Center for integrated Protein Science Munich (CiPSM), Ludwig-Maximilians-Universität München, Feodor-Lynen-Strasse 25, 81377 Munich, Germany.


Macromolecules

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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L2271Escherichia coliMutation(s): 0 
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Entity ID: 4
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50S ribosomal protein L3209Escherichia coliMutation(s): 0 
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Entity ID: 5
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50S ribosomal protein L4201Escherichia coliMutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L5177Escherichia coliMutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L6176Escherichia coliMutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L9149Escherichia coliMutation(s): 0 
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50S ribosomal protein L13I [auth J]142Escherichia coliMutation(s): 0 
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50S ribosomal protein L14J [auth K]122Escherichia coliMutation(s): 0 
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50S ribosomal protein L15K [auth L]143Escherichia coliMutation(s): 0 
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50S ribosomal protein L16L [auth M]136Escherichia coliMutation(s): 0 
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50S ribosomal protein L17M [auth N]120Escherichia coliMutation(s): 0 
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50S ribosomal protein L18N [auth O]116Escherichia coliMutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L19O [auth P]114Escherichia coliMutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L20P [auth Q]117Escherichia coliMutation(s): 0 
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Entity ID: 17
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50S ribosomal protein L21Q [auth R]103Escherichia coliMutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L22R [auth S]110Escherichia coliMutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L23S [auth T]93Escherichia coliMutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L24T [auth U]102Escherichia coliMutation(s): 0 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L25U [auth V]94Escherichia coliMutation(s): 0 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L27V [auth W]75Escherichia coliMutation(s): 0 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L28W [auth X]77Escherichia coliMutation(s): 0 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L29X [auth Y]63Escherichia coliMutation(s): 0 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L30Y [auth Z]58Escherichia coliMutation(s): 0 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L32Z [auth 0]56Escherichia coliMutation(s): 0 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L33AA [auth 1]50Escherichia coliMutation(s): 0 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L34BA [auth 2]46Escherichia coliMutation(s): 0 
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50S ribosomal protein L35CA [auth 3]64Escherichia coliMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L36DA [auth 4]38Escherichia coliMutation(s): 0 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L31EA [auth 6]66Escherichia coliMutation(s): 0 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S2GA [auth b]218Escherichia coliMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S3HA [auth c]206Escherichia coliMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S4IA [auth d]205Escherichia coliMutation(s): 0 
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Entity ID: 36
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30S ribosomal protein S5JA [auth e]157Escherichia coliMutation(s): 0 
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30S ribosomal protein S6KA [auth f]100Escherichia coliMutation(s): 0 
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30S ribosomal protein S7LA [auth g]151Escherichia coliMutation(s): 0 
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30S ribosomal protein S8MA [auth h]129Escherichia coliMutation(s): 0 
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30S ribosomal protein S9NA [auth i]127Escherichia coliMutation(s): 0 
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30S ribosomal protein S10OA [auth j]98Escherichia coliMutation(s): 0 
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30S ribosomal protein S11PA [auth k]116Escherichia coliMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S12QA [auth l]123Escherichia coliMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S13RA [auth m]114Escherichia coliMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S14SA [auth n]101Escherichia coliMutation(s): 0 
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S15TA [auth o]88Escherichia coliMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S16UA [auth p]82Escherichia coliMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S17VA [auth q]80Escherichia coliMutation(s): 0 
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S18WA [auth r]65Escherichia coliMutation(s): 0 
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UniProt GroupP0A7T7
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S19XA [auth s]79Escherichia coliMutation(s): 0 
UniProt
Find proteins for P0A7U3 (Escherichia coli (strain K12))
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UniProt GroupP0A7U3
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S20YA [auth t]85Escherichia coliMutation(s): 0 
UniProt
Find proteins for P0A7U7 (Escherichia coli (strain K12))
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UniProt GroupP0A7U7
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S21ZA [auth u]65Escherichia coliMutation(s): 0 
UniProt
Find proteins for P68679 (Escherichia coli (strain K12))
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UniProt GroupP68679
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Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
Alternative ribosome-rescue factor ABB [auth w]45Escherichia coliMutation(s): 0 
Gene Names: arfAyhdLb4550JW3253
UniProt
Find proteins for P36675 (Escherichia coli (strain K12))
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UniProt GroupP36675
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Entity ID: 56
MoleculeChains Sequence LengthOrganismDetailsImage
Peptide chain release factor 2DB [auth z]359Escherichia coliMutation(s): 0 
Gene Names: prfBsupKb2891JW5847
UniProt
Find proteins for P07012 (Escherichia coli (strain K12))
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UniProt GroupP07012
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Entity ID: 1
MoleculeChains LengthOrganismImage
23S ribosomal RNA2,903Escherichia coli
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Entity ID: 2
MoleculeChains LengthOrganismImage
5S ribosomal RNA120Escherichia coli
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Entity ID: 32
MoleculeChains LengthOrganismImage
16S ribosomal RNAFA [auth a]1,539Escherichia coli
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Entity ID: 53
MoleculeChains LengthOrganismImage
mRNAAB [auth v]6Escherichia coli
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Entity ID: 55
MoleculeChains LengthOrganismImage
P-site tRNACB [auth x]77Escherichia coli
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONFREALIGN9.11

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research FoundationGermanyFOR1805
German Research FoundationGermanyGRK1721

Revision History  (Full details and data files)

  • Version 1.0: 2016-12-14
    Type: Initial release
  • Version 1.1: 2017-02-08
    Changes: Database references
  • Version 1.2: 2017-08-30
    Changes: Author supporting evidence, Data collection, Derived calculations