› 6ysr

Electron Microscopy
3.1Å resolution

Structure of the P+9 stalled ribosome complex

Released:
DOI: 10.2210/pdb6ysr/pdb
PDB entry 6ysr coloured by chain, front view.
PDB entry 6ysr coloured by chain, side view.
PDB entry 6ysr coloured by chain, top view.
Source organism: Escherichia coli
Primary publication:
Mechanism of ribosome rescue by alternative ribosome-rescue factor B.
Chan KH, Petrychenko V, Mueller C, Maracci C, Holtkamp W, Wilson DN, Fischer N, Rodnina MV
OpenAccess logo Nat Commun 11 4106 (2020)
PMID: 32796827
Related structures: EMD-10905

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero 57-mer (preferred)
PDBe Complex ID:
PDB-CPX-241141 (preferred)
Entry contents:
52 distinct polypeptide molecules
5 distinct RNA molecules
Macromolecules (57 distinct):
Large ribosomal subunit protein bL32 Chain: 0
Molecule details ›
Chain: 0
Length: 57 amino acids
Theoretical weight: 6.46 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P0A7N4 (Residues: 1-57; Coverage: 100%)
Gene names: JW1075, b1089, rpmF
Sequence domains: Ribosomal L32p protein family
Large ribosomal subunit protein bL33 Chain: 1
Molecule details ›
Chain: 1
Length: 55 amino acids
Theoretical weight: 6.39 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P0A7N9 (Residues: 1-55; Coverage: 100%)
Gene names: JW3611, b3636, rpmG
Sequence domains: Ribosomal protein L33
Large ribosomal subunit protein bL34 Chain: 2
Large ribosomal subunit protein bL35 Chain: 3
Large ribosomal subunit protein bL36A Chain: 4
50S ribosomal protein L10 Chain: 5
50S ribosomal protein L31 Chain: 6
Large ribosomal subunit protein uL2 Chain: C
Large ribosomal subunit protein uL3 Chain: D
Large ribosomal subunit protein uL4 Chain: E
Large ribosomal subunit protein uL5 Chain: F
Large ribosomal subunit protein uL6 Chain: G
Large ribosomal subunit protein bL9 Chain: H
Large ribosomal subunit protein uL11 Chain: I
Large ribosomal subunit protein uL13 Chain: J
Large ribosomal subunit protein uL14 Chain: K
Large ribosomal subunit protein uL15 Chain: L
Large ribosomal subunit protein uL16 Chain: M
Large ribosomal subunit protein bL17 Chain: N
Large ribosomal subunit protein uL18 Chain: O
Large ribosomal subunit protein bL19 Chain: P
Large ribosomal subunit protein bL20 Chain: Q
Large ribosomal subunit protein bL21 Chain: R
Large ribosomal subunit protein uL22 Chain: S
Large ribosomal subunit protein uL23 Chain: T
Large ribosomal subunit protein uL24 Chain: U
Large ribosomal subunit protein bL25 Chain: V
Large ribosomal subunit protein bL27 Chain: W
Large ribosomal subunit protein bL28 Chain: X
Large ribosomal subunit protein uL29 Chain: Y
Large ribosomal subunit protein uL30 Chain: Z
Small ribosomal subunit protein uS2 Chain: b
Small ribosomal subunit protein uS3 Chain: c
Small ribosomal subunit protein uS4 Chain: d
Small ribosomal subunit protein uS5 Chain: e
30S ribosomal protein S6 Chain: f
30S ribosomal protein S7 Chain: g
Small ribosomal subunit protein uS8 Chain: h
Small ribosomal subunit protein uS9 Chain: i
Small ribosomal subunit protein uS10 Chain: j
Small ribosomal subunit protein uS11 Chain: k
Small ribosomal subunit protein uS12 Chain: l
Small ribosomal subunit protein uS13 Chain: m
Small ribosomal subunit protein uS14 Chain: n
Small ribosomal subunit protein uS15 Chain: o
Small ribosomal subunit protein bS16 Chain: p
Small ribosomal subunit protein uS17 Chain: q
Small ribosomal subunit protein bS18 Chain: r
Small ribosomal subunit protein uS19 Chain: s
Small ribosomal subunit protein bS20 Chain: t
Small ribosomal subunit protein bS21 Chain: u
P-site fMet-Phe-tRNA(Phe) Chain: v
23S ribosomal RNA Chain: A
5S ribosomal RNA Chain: B
16S ribosomal RNA Chain: a
P-site fMet-Phe-tRNA(Phe) Chain: w
Messenger RNA Chain: x

Ligands and Environments

4 bound ligands:
Ligand MG 332 x MG
Ligand ZN 2 x ZN
Ligand CL 1 x CL
Ligand NA 2 x NA
17 modified residues:
Ligand 1MG 1 x 1MG
Ligand PSU 13 x PSU
Ligand 5MC 4 x 5MC
Ligand 6MZ 2 x 6MZ
Ligand 2MG 5 x 2MG
Ligand 3TD 1 x 3TD
Ligand 5MU 2 x 5MU
Ligand G7M 3 x G7M
Ligand OMG 1 x OMG
Ligand OMC 1 x OMC
Ligand 2MA 1 x 2MA
Ligand OMU 1 x OMU
Ligand 4OC 1 x 4OC
Ligand UR3 1 x UR3
Ligand MA6 2 x MA6
Ligand 4SU 1 x 4SU
Ligand MIA 1 x MIA

Experiments and Validation Details

wwPDB Validation report is not available for this EM entry.
Resolution: 3.1Å
Relevant EMDB volumes: EMD-10905

Quick links

Citations

4 review citations

Maintaining mitochondrial ribosome function: The role of ribosome rescue and recycling factors.
Nadler et al. (2022)
3 more

1 mention without citation

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