› 7d6z

Electron Microscopy
3.4Å resolution

Molecular model of the cryo-EM structure of 70S ribosome in complex with peptide deformylase and trigger factor

Released:
DOI: 10.2210/pdb7d6z/pdb
PDB entry 7d6z coloured by chain, front view.
PDB entry 7d6z coloured by chain, side view.
PDB entry 7d6z coloured by chain, top view.
Source organisms:
Primary publication:
Structural insights into the interplay of protein biogenesis factors with the 70S ribosome.
Akbar S, Bhakta S, Sengupta J
Structure 29 755-767.e4 (2021)
PMID: 33761323
Related structures: EMD-30598

Function and Biology Details

Reactions catalysed: 
Formyl-L-methionyl peptide + H(2)O = formate + methionyl peptide
Peptidylproline (omega=180) = peptidylproline (omega=0)
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero 58-mer (preferred)
PDBe Complex ID:
PDB-CPX-279455 (preferred)
Entry contents:
52 distinct polypeptide molecules
6 distinct RNA molecules
Macromolecules (58 distinct):
Small ribosomal subunit protein bS20 Chain: 0
Molecule details ›
Chain: 0
Length: 87 amino acids
Theoretical weight: 9.71 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P0A7U7 (Residues: 1-87; Coverage: 100%)
Gene names: JW0022, b0023, rpsT
Sequence domains: Ribosomal protein S20
Small ribosomal subunit protein bS21 Chain: 1
Molecule details ›
Chain: 1
Length: 71 amino acids
Theoretical weight: 8.52 KDa
Source organism: Escherichia coli
UniProt:
  • Canonical: P68679 (Residues: 1-71; Coverage: 100%)
Gene names: JW3037, b3065, rpsU
Sequence domains: Ribosomal protein S21
Large ribosomal subunit protein bL31 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 uL30 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 uL23 Chain: Z
Large ribosomal subunit protein bL32 Chain: a
Large ribosomal subunit protein bL33 Chain: b
Large ribosomal subunit protein bL34 Chain: c
Large ribosomal subunit protein bL35 Chain: d
Large ribosomal subunit protein bL36A Chain: e
Peptide deformylase Chain: g
Trigger factor Chain: h
Small ribosomal subunit protein uS2 Chain: i
Small ribosomal subunit protein uS3 Chain: j
Small ribosomal subunit protein uS4 Chain: k
Small ribosomal subunit protein uS5 Chain: l
Small ribosomal subunit protein bS6 Chain: m
Small ribosomal subunit protein uS7 Chain: n
Small ribosomal subunit protein uS8 Chain: o
Small ribosomal subunit protein uS9 Chain: p
Small ribosomal subunit protein uS10 Chain: q
Small ribosomal subunit protein uS11 Chain: r
Small ribosomal subunit protein uS12 Chain: s
Small ribosomal subunit protein uS13 Chain: t
Small ribosomal subunit protein uS14 Chain: u
Small ribosomal subunit protein uS15 Chain: v
Small ribosomal subunit protein bS16 Chain: w
Small ribosomal subunit protein uS17 Chain: x
Small ribosomal subunit protein bS18 Chain: y
Small ribosomal subunit protein uS19 Chain: z
E-site tRNA Chain: 2
P-site tRNA Chain: 3
A-site tRNA Chain: 4
23S ribosomal rRNA Chain: A
5S ribosomal rRNA Chain: B
16S ribosomal rRNA Chain: f

Ligands and Environments

No bound ligands
10 modified residues:
Ligand 4SU 3 x 4SU
Ligand 6MZ 1 x 6MZ
Ligand 7MG 3 x 7MG
Ligand 5MU 3 x 5MU
Ligand PSU 5 x PSU
Ligand QUO 1 x QUO
Ligand 2MA 1 x 2MA
Ligand U8U 1 x U8U
Ligand T6A 1 x T6A
Ligand 3AU 1 x 3AU

Experiments and Validation Details

wwPDB Validation report is not available for this EM entry.
Resolution: 3.4Å
Relevant EMDB volumes: EMD-30598
Expression system: Escherichia coli

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Citations

1 review citation

Cotranslational Biogenesis of Membrane Proteins in Bacteria.
Mercier et al. (2022)
4 other articles