5U4J

Structural Basis of Co-translational Quality Control by ArfA and RF2 Bound to Ribosome


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.7 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.5 of the entry. See complete history

Literature

Structural basis of co-translational quality control by ArfA and RF2 bound to ribosome.

Zeng, F.Chen, Y.Remis, J.Shekhar, M.Phillips, J.C.Tajkhorshid, E.Jin, H.

(2017) Nature 541: 554-557

  • DOI: 10.1038/nature21053
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Quality control mechanisms intervene appropriately when defective translation events occur, in order to preserve the integrity of protein synthesis. Rescue of ribosomes translating on messenger RNAs that lack stop codons is one of the co-translationa ...

    Quality control mechanisms intervene appropriately when defective translation events occur, in order to preserve the integrity of protein synthesis. Rescue of ribosomes translating on messenger RNAs that lack stop codons is one of the co-translational quality control pathways. In many bacteria, ArfA recognizes stalled ribosomes and recruits the release factor RF2, which catalyses the termination of protein synthesis. Although an induced-fit mechanism of nonstop mRNA surveillance mediated by ArfA and RF2 has been reported, the molecular interaction between ArfA and RF2 in the ribosome that is responsible for the mechanism is unknown. Here we report an electron cryo-microscopy structure of ArfA and RF2 in complex with the 70S ribosome bound to a nonstop mRNA. The structure, which is consistent with our kinetic and biochemical data, reveals the molecular interactions that enable ArfA to specifically recruit RF2, not RF1, into the ribosome and to enable RF2 to release the truncated protein product in this co-translational quality control pathway. The positively charged C-terminal domain of ArfA anchors in the mRNA entry channel of the ribosome. Furthermore, binding of ArfA and RF2 induces conformational changes in the ribosomal decoding centre that are similar to those seen in other protein-involved decoding processes. Specific interactions between residues in the N-terminal domain of ArfA and RF2 help RF2 to adopt a catalytically competent conformation for peptide release. Our findings provide a framework for understanding recognition of the translational state of the ribosome by new proteins, and expand our knowledge of the decoding potential of the ribosome.


    Organizational Affiliation

    Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S3
c
233Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsC
Find proteins for P0A7V3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7V3
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S4
d
206Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsD (ramA)
Find proteins for P0A7V8 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7V8
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S5
e
167Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsE (spc)
Find proteins for P0A7W1 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7W1
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S12
l
124Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsL (strA)
Find proteins for P0A7S3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7S3
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
Peptide chain release factor 2
v
383Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: prfB (supK)
Find proteins for P07012 (Escherichia coli (strain K12))
Go to UniProtKB:  P07012
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
Alternative ribosome-rescue factor A
w
57Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: arfA (yhdL)
Find proteins for P36675 (Escherichia coli (strain K12))
Go to UniProtKB:  P36675
Entity ID: 1
MoleculeChainsLengthOrganism
16S rRNAa1533Escherichia coli
Entity ID: 2
MoleculeChainsLengthOrganism
23S rRNAA2904Escherichia coli
Entity ID: 6
MoleculeChainsLengthOrganism
mRNAz18Escherichia coli
Entity ID: 7
MoleculeChainsLengthOrganism
P-site tRNA fMetx77Escherichia coli
Small Molecules
Modified Residues  13 Unique
IDChainsTypeFormula2D DiagramParent
PSU
Query on PSU
a, A
RNA LINKINGC9 H13 N2 O9 PU
5MC
Query on 5MC
A, a
RNA LINKINGC10 H16 N3 O8 PC
OMU
Query on OMU
A
RNA LINKINGC10 H15 N2 O9 PU
1MG
Query on 1MG
A
RNA LINKINGC11 H16 N5 O8 PG
OMC
Query on OMC
A
RNA LINKINGC10 H16 N3 O8 PC
MA6
Query on MA6
a
RNA LINKINGC12 H18 N5 O7 PA
2MG
Query on 2MG
A, a
RNA LINKINGC11 H16 N5 O8 PG
G7M
Query on G7M
a, A
RNA LINKINGC11 H17 N5 O8 PG
UR3
Query on UR3
a
RNA LINKINGC10 H15 N2 O9 PU
OMG
Query on OMG
A
RNA LINKINGC11 H16 N5 O8 PG
5MU
Query on 5MU
A
RNA LINKINGC10 H15 N2 O9 PU
2MA
Query on 2MA
A
RNA LINKINGC11 H16 N5 O7 PA
4OC
Query on 4OC
a
RNA LINKINGC11 H18 N3 O8 PC
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.7 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesR01GM120552

Revision History 

  • Version 1.0: 2017-01-11
    Type: Initial release
  • Version 1.1: 2017-01-25
    Type: Database references
  • Version 1.2: 2017-02-08
    Type: Database references
  • Version 1.3: 2017-09-27
    Type: Author supporting evidence, Data collection
  • Version 1.4: 2018-07-18
    Type: Data collection, Experimental preparation
  • Version 1.5: 2018-10-03
    Type: Data collection, Other, Refinement description