› 7pjv

Electron Microscopy
3.1Å resolution

Structure of the 70S-EF-G-GDP-Pi ribosome complex with tRNAs in hybrid state 1 (H1-EF-G-GDP-Pi)

Released:
DOI: 10.2210/pdb7pjv/pdb
PDB entry 7pjv coloured by chain, front view.
PDB entry 7pjv coloured by chain, side view.
PDB entry 7pjv coloured by chain, top view.
Source organism: Escherichia coli K-12
Primary publication:
Structural mechanism of GTPase-powered ribosome-tRNA movement.
Petrychenko V, Peng BZ, de A P Schwarzer AC, Peske F, Rodnina MV, Fischer N
OpenAccess logo Nat Commun 12 5933 (2021)
PMID: 34635670
Related structures: EMD-13461

Function and Biology Details

Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero 59-mer (preferred)
PDBe Complex ID:
PDB-CPX-135494 (preferred)
Entry contents:
53 distinct polypeptide molecules
6 distinct RNA molecules
Macromolecules (59 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 K-12
Large ribosomal subunit protein bL33 Chain: 1
Molecule details ›
Chain: 1
Length: 55 amino acids
Theoretical weight: 6.39 KDa
Source organism: Escherichia coli K-12
Large ribosomal subunit protein bL34 Chain: 2
Molecule details ›
Chain: 2
Length: 46 amino acids
Theoretical weight: 5.4 KDa
Source organism: Escherichia coli K-12
Large ribosomal subunit protein bL35 Chain: 3
Molecule details ›
Chain: 3
Length: 65 amino acids
Theoretical weight: 7.31 KDa
Source organism: Escherichia coli K-12
Large ribosomal subunit protein bL36A Chain: 4
Molecule details ›
Chain: 4
Length: 38 amino acids
Theoretical weight: 4.38 KDa
Source organism: Escherichia coli K-12
Large ribosomal subunit protein uL10 Chain: 5
Molecule details ›
Chain: 5
Length: 165 amino acids
Theoretical weight: 17.74 KDa
Source organism: Escherichia coli K-12
Large ribosomal subunit protein bL31 Chain: 6
Molecule details ›
Chain: 6
Length: 70 amino acids
Theoretical weight: 7.89 KDa
Source organism: Escherichia coli K-12
Large ribosomal subunit protein uL2 Chain: C
Molecule details ›
Chain: C
Length: 273 amino acids
Theoretical weight: 29.92 KDa
Source organism: Escherichia coli K-12
Large ribosomal subunit protein uL3 Chain: D
Molecule details ›
Chain: D
Length: 209 amino acids
Theoretical weight: 22.28 KDa
Source organism: Escherichia coli K-12
Large ribosomal subunit protein uL4 Chain: E
Molecule details ›
Chain: E
Length: 201 amino acids
Theoretical weight: 22.12 KDa
Source organism: Escherichia coli K-12
Large ribosomal subunit protein uL5 Chain: F
Molecule details ›
Chain: F
Length: 179 amino acids
Theoretical weight: 20.33 KDa
Source organism: Escherichia coli K-12
Large ribosomal subunit protein uL6 Chain: G
Molecule details ›
Chain: G
Length: 177 amino acids
Theoretical weight: 18.93 KDa
Source organism: Escherichia coli K-12
Large ribosomal subunit protein bL9 Chain: H
Molecule details ›
Chain: H
Length: 149 amino acids
Theoretical weight: 15.79 KDa
Source organism: Escherichia coli K-12
Large ribosomal subunit protein uL11 Chain: I
Molecule details ›
Chain: I
Length: 142 amino acids
Theoretical weight: 14.89 KDa
Source organism: Escherichia coli K-12
Large ribosomal subunit protein uL13 Chain: J
Molecule details ›
Chain: J
Length: 142 amino acids
Theoretical weight: 16.05 KDa
Source organism: Escherichia coli K-12
Large ribosomal subunit protein uL14 Chain: K
Molecule details ›
Chain: K
Length: 123 amino acids
Theoretical weight: 13.57 KDa
Source organism: Escherichia coli K-12
Large ribosomal subunit protein uL15 Chain: L
Molecule details ›
Chain: L
Length: 144 amino acids
Theoretical weight: 15.01 KDa
Source organism: Escherichia coli K-12
Large ribosomal subunit protein uL16 Chain: M
Molecule details ›
Chain: M
Length: 136 amino acids
Theoretical weight: 15.31 KDa
Source organism: Escherichia coli K-12
Large ribosomal subunit protein bL17 Chain: N
Molecule details ›
Chain: N
Length: 127 amino acids
Theoretical weight: 14.39 KDa
Source organism: Escherichia coli K-12
Large ribosomal subunit protein uL18 Chain: O
Molecule details ›
Chain: O
Length: 117 amino acids
Theoretical weight: 12.79 KDa
Source organism: Escherichia coli K-12
Large ribosomal subunit protein bL19 Chain: P
Molecule details ›
Chain: P
Length: 115 amino acids
Theoretical weight: 13.16 KDa
Source organism: Escherichia coli K-12
Large ribosomal subunit protein bL20 Chain: Q
Molecule details ›
Chain: Q
Length: 118 amino acids
Theoretical weight: 13.53 KDa
Source organism: Escherichia coli K-12
Large ribosomal subunit protein bL21 Chain: R
Molecule details ›
Chain: R
Length: 103 amino acids
Theoretical weight: 11.59 KDa
Source organism: Escherichia coli K-12
Large ribosomal subunit protein uL22 Chain: S
Molecule details ›
Chain: S
Length: 110 amino acids
Theoretical weight: 12.25 KDa
Source organism: Escherichia coli K-12
Large ribosomal subunit protein uL23 Chain: T
Molecule details ›
Chain: T
Length: 100 amino acids
Theoretical weight: 11.22 KDa
Source organism: Escherichia coli K-12
Large ribosomal subunit protein uL24 Chain: U
Molecule details ›
Chain: U
Length: 104 amino acids
Theoretical weight: 11.34 KDa
Source organism: Escherichia coli K-12
Large ribosomal subunit protein bL25 Chain: V
Molecule details ›
Chain: V
Length: 94 amino acids
Theoretical weight: 10.71 KDa
Source organism: Escherichia coli K-12
Large ribosomal subunit protein bL27 Chain: W
Molecule details ›
Chain: W
Length: 85 amino acids
Theoretical weight: 9.15 KDa
Source organism: Escherichia coli K-12
Large ribosomal subunit protein bL28 Chain: X
Molecule details ›
Chain: X
Length: 78 amino acids
Theoretical weight: 9.03 KDa
Source organism: Escherichia coli K-12
Large ribosomal subunit protein uL29 Chain: Y
Molecule details ›
Chain: Y
Length: 63 amino acids
Theoretical weight: 7.29 KDa
Source organism: Escherichia coli K-12
Large ribosomal subunit protein uL30 Chain: Z
Molecule details ›
Chain: Z
Length: 59 amino acids
Theoretical weight: 6.55 KDa
Source organism: Escherichia coli K-12
Small ribosomal subunit protein uS2 Chain: b
Molecule details ›
Chain: b
Length: 240 amino acids
Theoretical weight: 26.65 KDa
Source organism: Escherichia coli K-12
Small ribosomal subunit protein uS3 Chain: c
Molecule details ›
Chain: c
Length: 233 amino acids
Theoretical weight: 26.03 KDa
Source organism: Escherichia coli K-12
Small ribosomal subunit protein uS4 Chain: d
Molecule details ›
Chain: d
Length: 206 amino acids
Theoretical weight: 23.51 KDa
Source organism: Escherichia coli K-12
Small ribosomal subunit protein uS5 Chain: e
Molecule details ›
Chain: e
Length: 167 amino acids
Theoretical weight: 17.63 KDa
Source organism: Escherichia coli K-12
Small ribosomal subunit protein bS6 Chain: f
Molecule details ›
Chain: f
Length: 135 amino acids
Theoretical weight: 15.73 KDa
Source organism: Escherichia coli K-12
Small ribosomal subunit protein uS7 Chain: g
Molecule details ›
Chain: g
Length: 179 amino acids
Theoretical weight: 20.06 KDa
Source organism: Escherichia coli K-12
Small ribosomal subunit protein uS8 Chain: h
Molecule details ›
Chain: h
Length: 130 amino acids
Theoretical weight: 14.15 KDa
Source organism: Escherichia coli K-12
Small ribosomal subunit protein uS9 Chain: i
Molecule details ›
Chain: i
Length: 130 amino acids
Theoretical weight: 14.89 KDa
Source organism: Escherichia coli K-12
Small ribosomal subunit protein uS10 Chain: j
Molecule details ›
Chain: j
Length: 103 amino acids
Theoretical weight: 11.76 KDa
Source organism: Escherichia coli K-12
Small ribosomal subunit protein uS11 Chain: k
Molecule details ›
Chain: k
Length: 129 amino acids
Theoretical weight: 13.87 KDa
Source organism: Escherichia coli K-12
Small ribosomal subunit protein uS12 Chain: l
Molecule details ›
Chain: l
Length: 124 amino acids
Theoretical weight: 13.77 KDa
Source organism: Escherichia coli K-12
Small ribosomal subunit protein uS13 Chain: m
Molecule details ›
Chain: m
Length: 118 amino acids
Theoretical weight: 13.13 KDa
Source organism: Escherichia coli K-12
Small ribosomal subunit protein uS14 Chain: n
Molecule details ›
Chain: n
Length: 102 amino acids
Theoretical weight: 11.68 KDa
Source organism: Escherichia coli K-12
Small ribosomal subunit protein uS15 Chain: o
Molecule details ›
Chain: o
Length: 89 amino acids
Theoretical weight: 10.29 KDa
Source organism: Escherichia coli K-12
Small ribosomal subunit protein bS16 Chain: p
Molecule details ›
Chain: p
Length: 82 amino acids
Theoretical weight: 9.21 KDa
Source organism: Escherichia coli K-12
Small ribosomal subunit protein uS17 Chain: q
Molecule details ›
Chain: q
Length: 84 amino acids
Theoretical weight: 9.72 KDa
Source organism: Escherichia coli K-12
30S ribosomal protein S18 Chain: r
Molecule details ›
Chain: r
Length: 75 amino acids
Theoretical weight: 9.01 KDa
Source organism: Escherichia coli K-12
Small ribosomal subunit protein uS19 Chain: s
Molecule details ›
Chain: s
Length: 92 amino acids
Theoretical weight: 10.46 KDa
Source organism: Escherichia coli K-12
Small ribosomal subunit protein bS20 Chain: t
Molecule details ›
Chain: t
Length: 87 amino acids
Theoretical weight: 9.71 KDa
Source organism: Escherichia coli K-12
Small ribosomal subunit protein bS21 Chain: u
Molecule details ›
Chain: u
Length: 71 amino acids
Theoretical weight: 8.52 KDa
Source organism: Escherichia coli K-12
Elongation factor G Chain: x
Molecule details ›
Chain: x
Length: 704 amino acids
Theoretical weight: 77.68 KDa
Source organism: Escherichia coli K-12
Dipeptide (FME-PHE) Chain: y
Molecule details ›
Chain: y
Length: 2 amino acids
Theoretical weight: 324 Da
Source organism: Escherichia coli K-12
23S ribosomal RNA Chain: A
Molecule details ›
Chain: A
Length: 2903 nucleotides
Theoretical weight: 941.54 KDa
Source organism: Escherichia coli K-12
Sequence domains: Bacterial large subunit ribosomal RNA
5S ribosomal RNA Chain: B
Molecule details ›
Chain: B
Length: 120 nucleotides
Theoretical weight: 38.79 KDa
Source organism: Escherichia coli K-12
Sequence domains: 5S ribosomal RNA
16S ribosomal RNA Chain: a
Molecule details ›
Chain: a
Length: 1542 nucleotides
Theoretical weight: 499.87 KDa
Source organism: Escherichia coli K-12
Sequence domains: Bacterial small subunit ribosomal RNA
P-site tRNA(fMet) Chain: v
Molecule details ›
Chain: v
Length: 77 nucleotides
Theoretical weight: 24.82 KDa
Source organism: Escherichia coli K-12
Sequence domains: tRNA
P-site fMet-Phe-tRNA(Phe) Chain: w
Molecule details ›
Chain: w
Length: 76 nucleotides
Theoretical weight: 24.64 KDa
Source organism: Escherichia coli K-12
Sequence domains: tRNA
Messenger RNA Chain: z
Molecule details ›
Chain: z
Length: 33 nucleotides
Theoretical weight: 10.48 KDa
Source organism: Escherichia coli K-12

Ligands and Environments

6 bound ligands:
Ligand MG 369 x MG
Ligand ZN 2 x ZN
Ligand NA 2 x NA
Ligand AM2 3 x AM2
Ligand GDP 1 x GDP
Ligand PO4 1 x PO4
19 modified residues:
Ligand 1MG 1 x 1MG
Ligand PSU 14 x PSU
Ligand 5MC 4 x 5MC
Ligand 6MZ 2 x 6MZ
Ligand 2MG 5 x 2MG
Ligand 3TD 1 x 3TD
Ligand 5MU 3 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 2 x 4SU
Ligand H2U 1 x H2U
Ligand MIA 1 x MIA
Ligand FME 1 x FME

Experiments and Validation Details

Entry percentile scores
Resolution: 3.1Å
Relevant EMDB volumes: EMD-13461

Quick links

Citations

3 review citations

The Structural Dynamics of Translation.
Korostelev AA. (2022)
2 more

7 mentions without citation

Visualizing translation dynamics at atomic detail inside a bacterial cell.
Xue et al. (2022)
6 more