› 8fzf

Electron Microscopy
3.2Å resolution

Cryo-EM structure of an E. coli rotated ribosome complex bound with RF3-ppGpp and p/E-tRNAPhe (Composite state I-C)

Released:
DOI: 10.2210/pdb8fzf/pdb
PDB entry 8fzf coloured by chain, front view.
PDB entry 8fzf coloured by chain, side view.
PDB entry 8fzf coloured by chain, top view.
Source organisms:
Primary publication:
The ribosome termination complex remodels release factor RF3 and ejects GDP.
Li L, Rybak MY, Lin J, Gagnon MG
Nat Struct Mol Biol (2024)
PMID: 39030416
Related structures: EMD-29624

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero 56-mer (preferred)
PDBe Complex ID:
PDB-CPX-301554 (preferred)
Entry contents:
51 distinct polypeptide molecules
5 distinct RNA molecules
Macromolecules (56 distinct):
Small ribosomal subunit protein uS2 Chain: b
Molecule details ›
Chain: b
Length: 241 amino acids
Theoretical weight: 26.8 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P0A7V0 (Residues: 1-241; Coverage: 100%)
Gene names: JW0164, b0169, rpsB
Sequence domains: Ribosomal protein S2
Small ribosomal subunit protein uS3 Chain: c
Molecule details ›
Chain: c
Length: 233 amino acids
Theoretical weight: 26.03 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P0A7V3 (Residues: 1-233; Coverage: 100%)
Gene names: JW3276, b3314, rpsC
Sequence domains:
Small ribosomal subunit protein uS4 Chain: d
Small ribosomal subunit protein uS5 Chain: e
Small ribosomal subunit protein bS6 Chain: f
Small ribosomal subunit protein uS7 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
Peptide chain release factor RF3 Chain: v
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 uL10 Chain: I
Large ribosomal subunit protein uL11 Chain: J
Large ribosomal subunit protein uL13 Chain: L
Large ribosomal subunit protein uL14 Chain: M
Large ribosomal subunit protein uL15 Chain: N
Large ribosomal subunit protein uL16 Chain: O
Large ribosomal subunit protein bL17 Chain: P
Large ribosomal subunit protein uL18 Chain: Q
Large ribosomal subunit protein bL19 Chain: R
Large ribosomal subunit protein bL20 Chain: S
Large ribosomal subunit protein bL21 Chain: T
Large ribosomal subunit protein uL22 Chain: U
Large ribosomal subunit protein uL23 Chain: V
Large ribosomal subunit protein uL24 Chain: W
Large ribosomal subunit protein bL25 Chain: X
Large ribosomal subunit protein bL27 Chain: Y
Large ribosomal subunit protein bL28 Chain: Z
Large ribosomal subunit protein uL29 Chain: 1
Large ribosomal subunit protein uL30 Chain: 2
Large ribosomal subunit protein bL31 Chain: 3
Large ribosomal subunit protein bL32 Chain: 4
Large ribosomal subunit protein bL33 Chain: 5
Large ribosomal subunit protein bL34 Chain: 6
Large ribosomal subunit protein bL35 Chain: 7
Large ribosomal subunit protein bL36A Chain: 8
16S ribosomal RNA Chain: a
p/E phenylalanyl-tRNA Chain: x
F-UAA mRNA Chain: z
23S ribosomal RNA Chain: A
5S ribosomal RNA Chain: B

Ligands and Environments

3 bound ligands:
Ligand MG 384 x MG
Ligand G4P 1 x G4P
Ligand ZN 2 x ZN
21 modified residues:
Ligand PSU 13 x PSU
Ligand G7M 3 x G7M
Ligand 2MG 5 x 2MG
Ligand 5MC 3 x 5MC
Ligand 4OC 1 x 4OC
Ligand UR3 1 x UR3
Ligand MA6 2 x MA6
Ligand IAS 1 x IAS
Ligand D2T 1 x D2T
Ligand 4SU 1 x 4SU
Ligand MIA 1 x MIA
Ligand 5MU 3 x 5MU
Ligand 1MG 1 x 1MG
Ligand 6MZ 2 x 6MZ
Ligand 3TD 1 x 3TD
Ligand OMG 1 x OMG
Ligand H2U 1 x H2U
Ligand OMC 1 x OMC
Ligand 2MA 1 x 2MA
Ligand OMU 1 x OMU
Ligand 4D4 1 x 4D4

Experiments and Validation Details

wwPDB Validation report is not available for this EM entry.
Resolution: 3.2Å
Relevant EMDB volumes: EMD-29624
Expression system: Escherichia coli BL21(DE3)

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