6C4H

Conformation of methylated GGQ in the peptidyl transferase center during translation termination (PTC region)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.1 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 2.0 of the entry. See complete history

Literature

Conformation of methylated GGQ in the Peptidyl Transferase Center during Translation Termination.

Zeng, F.Jin, H.

(2018) Sci Rep 8: 2349-2349

  • DOI: 10.1038/s41598-018-20107-8
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The universally conserved Gly-Gly-Gln (GGQ) tripeptide in release factors or release factor-like surveillance proteins is required to catalyze the release of nascent peptide in the ribosome. The glutamine of the GGQ is methylated post-translationally ...

    The universally conserved Gly-Gly-Gln (GGQ) tripeptide in release factors or release factor-like surveillance proteins is required to catalyze the release of nascent peptide in the ribosome. The glutamine of the GGQ is methylated post-translationally at the N 5 position in vivo; this covalent modification is essential for optimal cell growth and efficient translation termination. However, the precise conformation of the methylated-GGQ tripeptide in the ribosome remains unknown. Using cryoEM and X-ray crystallography, we report the conformation of methylated-GGQ in the peptidyl transferase center of the ribosome during canonical translational termination and co-translation quality control. It has been suggested that the GGQ motif arose independently through convergent evolution among otherwise unrelated proteins that catalyze peptide release. The requirement for this tripeptide in the highly conserved peptidyl transferase center suggests that the conformation reported here is likely shared during termination of protein synthesis in all domains of life.


    Organizational Affiliation

    Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, USA. hjin@illinois.edu.,Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, USA. hjin@illinois.edu.,Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L2
C
273Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplB
Find proteins for P60422 (Escherichia coli (strain K12))
Go to UniProtKB:  P60422
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L3
D
209Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplC
Find proteins for P60438 (Escherichia coli (strain K12))
Go to UniProtKB:  P60438
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L16
N
136Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplP
Find proteins for P0ADY7 (Escherichia coli (strain K12))
Go to UniProtKB:  P0ADY7
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L27
X
85Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpmA
Find proteins for P0A7L8 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7L8
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
Peptide chain release factor RF2
v
384Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: prfB (supK)
Find proteins for P07012 (Escherichia coli (strain K12))
Go to UniProtKB:  P07012
Entity ID: 1
MoleculeChainsLengthOrganism
23S rRNAA2904Escherichia coli
Entity ID: 6
MoleculeChainsLengthOrganism
P-site tRNA fMetx77Escherichia coli
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  13 Unique
IDChainsTypeFormula2D DiagramParent
PSU
Query on PSU
A
RNA LINKINGC9 H13 N2 O9 PU
5MC
Query on 5MC
A
RNA LINKINGC10 H16 N3 O8 PC
6MZ
Query on 6MZ
A
RNA LINKINGC11 H16 N5 O7 PA
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
2MG
Query on 2MG
A
RNA LINKINGC11 H16 N5 O8 PG
G7M
Query on G7M
A
RNA LINKINGC11 H17 N5 O8 PG
MEQ
Query on MEQ
v
L-PEPTIDE LINKINGC6 H12 N2 O3GLN
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
3TD
Query on 3TD
A
RNA LINKINGC10 H15 N2 O9 PU
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.1 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2018-01-12 
  • Released Date: 2018-02-21 
  • Deposition Author(s): Zeng, F., Jin, H.

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01-GM120552

Revision History 

  • Version 1.0: 2018-02-21
    Type: Initial release
  • Version 1.1: 2018-02-28
    Type: Author supporting evidence
  • Version 2.0: 2020-01-08
    Type: Author supporting evidence, Polymer sequence