› 6c4h

Electron Microscopy
3.1Å resolution

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

Released:
DOI: 10.2210/pdb6c4h/pdb
PDB entry 6c4h coloured by chain, front view.
PDB entry 6c4h coloured by chain, side view.
PDB entry 6c4h coloured by chain, top view.
Source organism: Escherichia coli
Primary publication:
Conformation of methylated GGQ in the Peptidyl Transferase Center during Translation Termination.
Zeng F, Jin H
Sci Rep 8 2349 (2018)
PMID: 29403017
Related structures: EMD-7340

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero heptamer (preferred)
PDBe Complex ID:
PDB-CPX-139337 (preferred)
Entry contents:
5 distinct polypeptide molecules
2 distinct RNA molecules
Macromolecules (7 distinct):
Large ribosomal subunit protein uL2 Chain: C
Molecule details ›
Chain: C
Length: 273 amino acids
Theoretical weight: 29.92 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P60422 (Residues: 1-273; Coverage: 100%)
Gene names: JW3279, b3317, rplB
Sequence domains:
Large ribosomal subunit protein uL3 Chain: D
Molecule details ›
Chain: D
Length: 209 amino acids
Theoretical weight: 22.28 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P60438 (Residues: 1-209; Coverage: 100%)
Gene names: JW3282, b3320, rplC
Sequence domains: Ribosomal protein L3
Large ribosomal subunit protein uL16 Chain: N
Molecule details ›
Chain: N
Length: 136 amino acids
Theoretical weight: 15.31 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P0ADY7 (Residues: 1-136; Coverage: 100%)
Gene names: JW3275, b3313, rplP
Sequence domains: Ribosomal protein L16p/L10e
Large ribosomal subunit protein bL27 Chain: X
Molecule details ›
Chain: X
Length: 85 amino acids
Theoretical weight: 9.15 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P0A7L8 (Residues: 1-85; Coverage: 100%)
Gene names: JW3152, b3185, rpmA
Sequence domains: Ribosomal L27 protein
Peptide chain release factor RF2 Chain: v
Molecule details ›
Chain: v
Length: 384 amino acids
Theoretical weight: 43.38 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli
UniProt:
  • Canonical: P07012 (Residues: 1-365; Coverage: 100%)
Gene names: JW5847, b2891, prfB, supK
Sequence domains:
Structure domains: Double Stranded RNA Binding Domain
23S ribosomal RNA Chain: A
Molecule details ›
Chain: A
Length: 2904 nucleotides
Theoretical weight: 941.82 KDa
Sequence domains: Bacterial large subunit ribosomal RNA
P-site tRNA fMet Chain: x
Molecule details ›
Chain: x
Length: 77 nucleotides
Theoretical weight: 24.79 KDa
Sequence domains: tRNA

Ligands and Environments

1 bound ligand:
Ligand MG 34 x MG
12 modified residues:
Ligand 1MG 1 x 1MG
Ligand PSU 8 x PSU
Ligand 5MU 2 x 5MU
Ligand 6MZ 1 x 6MZ
Ligand 2MG 2 x 2MG
Ligand 3TD 1 x 3TD
Ligand 5MC 1 x 5MC
Ligand G7M 1 x G7M
Ligand OMG 1 x OMG
Ligand OMC 1 x OMC
Ligand 2MA 1 x 2MA
Ligand OMU 1 x OMU

Experiments and Validation Details

Entry percentile scores
Resolution: 3.1Å
Relevant EMDB volumes: EMD-7340
Expression system: Escherichia coli

Quick links

Citations

1 review citation

Ribosome Rescue Pathways in Bacteria.
Müller et al. (2021)
7 other articles

1 mention without citation

Conformation of methylated GGQ in the Peptidyl Transferase Center during Translation Termination.
Zeng et al. (2018)