› 7pju

Electron Microscopy
9.5Å resolution

Structure of the 70S ribosome with tRNAs in hybrid state 2 (H2)

Released:
DOI: 10.2210/pdb7pju/pdb
PDB entry 7pju coloured by chain, front view.
PDB entry 7pju coloured by chain, side view.
PDB entry 7pju 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
Nat Commun 12 5933 (2021)
PMID: 34635670
Related structures: EMD-13460

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero 58-mer (preferred)
PDBe Complex ID:
PDB-CPX-240964 (preferred)
Entry contents:
52 distinct polypeptide molecules
6 distinct RNA molecules
Macromolecules (58 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
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 K-12
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
Molecule details ›
Chain: 2
Length: 46 amino acids
Theoretical weight: 5.4 KDa
Source organism: Escherichia coli K-12
UniProt:
  • Canonical: P0A7P5 (Residues: 1-46; Coverage: 100%)
Gene names: JW3680, b3703, rimA, rpmH, ssaF
Sequence domains: Ribosomal protein L34
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
UniProt:
  • Canonical: P0A7Q1 (Residues: 1-65; Coverage: 100%)
Gene names: JW1707, b1717, rpmI
Sequence domains: Ribosomal protein L35
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
UniProt:
  • Canonical: P0A7Q6 (Residues: 1-38; Coverage: 100%)
Gene names: JW3261, b3299, rpmJ
Sequence domains: Ribosomal protein L36
50S ribosomal protein L10 Chain: 5
Molecule details ›
Chain: 5
Length: 165 amino acids
Theoretical weight: 17.74 KDa
Source organism: Escherichia coli K-12
50S ribosomal protein L31 Chain: 6
Molecule details ›
Chain: 6
Length: 70 amino acids
Theoretical weight: 7.89 KDa
Source organism: Escherichia coli K-12
50S ribosomal protein L2 Chain: C
Molecule details ›
Chain: C
Length: 273 amino acids
Theoretical weight: 29.92 KDa
Source organism: Escherichia coli K-12
50S ribosomal protein L3 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
UniProt:
  • Canonical: F4T4K4 (Residues: 1-201; Coverage: 100%)
Gene names: ECIG_02561, rplD
Sequence domains: Ribosomal protein L4/L1 family
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
UniProt:
  • Canonical: F4VJU9 (Residues: 1-179; Coverage: 100%)
Gene names: ECPG_02628, rplE
Sequence domains:
50S ribosomal protein L6 Chain: G
Molecule details ›
Chain: G
Length: 177 amino acids
Theoretical weight: 18.93 KDa
Source organism: Escherichia coli K-12
50S ribosomal protein L9 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
UniProt:
  • Canonical: A0A7U9AQU6 (Residues: 1-142; Coverage: 100%)
Gene names: ECKG_05000, rplK
Sequence domains:
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
UniProt:
  • Canonical: D8A920 (Residues: 1-142; Coverage: 100%)
Gene names: HMPREF9530_03046, rplM
Sequence domains: Ribosomal protein L13
50S ribosomal protein L14 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
UniProt:
  • Canonical: A0A037Y8L6 (Residues: 1-144; Coverage: 100%)
Gene names: ACU57_21045, BANRA_01932, BGM66_003610, BJI68_08760, C0P57_002651, CIG67_10760, CTR35_003613, DTL43_21000, E4K51_21490, EIZ93_12470, FOI11_019260, FOI11_03920, FWK02_06270, G3V95_19845, G4A38_21510, G4A47_20780, GNW61_16630, GOP25_22705, GP954_00945, GP965_04295, GP979_02005, GRW05_09060, GRW56_00295, GRW57_03540, HMV95_19605, HVY77_02175, J0541_004396, JNP96_25305, NCTC11126_02772, NCTC9045_00567, NCTC9117_00757, NCTC9706_02738, QDW62_02195, RZR61_12890, rplO
Sequence domains: Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A
50S ribosomal protein L16 Chain: M
Molecule details ›
Chain: M
Length: 136 amino acids
Theoretical weight: 15.31 KDa
Source organism: Escherichia coli K-12
50S ribosomal protein L17 Chain: N
Molecule details ›
Chain: N
Length: 127 amino acids
Theoretical weight: 14.39 KDa
Source organism: Escherichia coli K-12
50S ribosomal protein L18 Chain: O
Molecule details ›
Chain: O
Length: 117 amino acids
Theoretical weight: 12.79 KDa
Source organism: Escherichia coli K-12
50S ribosomal protein L19 Chain: P
Molecule details ›
Chain: P
Length: 115 amino acids
Theoretical weight: 13.16 KDa
Source organism: Escherichia coli K-12
50S ribosomal protein L20 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
UniProt:
  • Canonical: D7XN42 (Residues: 1-103; Coverage: 100%)
Gene names: HMPREF9536_02456, rplU
Sequence domains: Ribosomal prokaryotic L21 protein
Ribosomal protein L22 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
UniProt:
  • Canonical: F4VJV9 (Residues: 1-100; Coverage: 100%)
Gene names: ECPG_02638, rplW
Sequence domains: Ribosomal protein L23
Ribosomal protein L24 Chain: U
Molecule details ›
Chain: U
Length: 104 amino acids
Theoretical weight: 11.34 KDa
Source organism: Escherichia coli K-12
50S ribosomal protein L25 Chain: V
Molecule details ›
Chain: V
Length: 94 amino acids
Theoretical weight: 10.71 KDa
Source organism: Escherichia coli K-12
50S ribosomal protein L27 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
UniProt:
  • Canonical: A0A4P8BWQ5 (Residues: 1-78; Coverage: 100%)
Gene names: CCU01_000655, rpmB
Sequence domains: Ribosomal L28 family
50S ribosomal protein L29 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
UniProt:
  • Canonical: S1ELC8 (Residues: 1-59; Coverage: 100%)
Gene names: A1UI_03575, rpmD
Sequence domains: Ribosomal protein L30p/L7e
30S ribosomal protein S2 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
UniProt:
  • Canonical: A0A0E1M2F3 (Residues: 1-233; Coverage: 100%)
Gene names: EC1303_c34600, rpsC
Sequence domains:
Ribosomal protein S4 Chain: d
Molecule details ›
Chain: d
Length: 206 amino acids
Theoretical weight: 23.51 KDa
Source organism: Escherichia coli K-12
30S ribosomal protein S5 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
UniProt:
  • Canonical: P02358 (Residues: 1-135; Coverage: 100%)
Gene names: JW4158, b4200, rpsF
Sequence domains: Ribosomal protein S6
30S ribosomal protein S7 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
UniProt:
  • Canonical: D8A1L7 (Residues: 1-130; Coverage: 100%)
Gene names: HMPREF9530_00381, rpsH
Sequence domains: Ribosomal protein S8
30S ribosomal protein S9 Chain: i
Molecule details ›
Chain: i
Length: 130 amino acids
Theoretical weight: 14.89 KDa
Source organism: Escherichia coli K-12
30S ribosomal protein S10 Chain: j
Molecule details ›
Chain: j
Length: 103 amino acids
Theoretical weight: 11.76 KDa
Source organism: Escherichia coli K-12
30S ribosomal protein S11 Chain: k
Molecule details ›
Chain: k
Length: 129 amino acids
Theoretical weight: 13.87 KDa
Source organism: Escherichia coli K-12
30S ribosomal protein S12 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
UniProt:
  • Canonical: B7LHZ5 (Residues: 1-118; Coverage: 100%)
Gene names: EC55989_3715, rpsM
Sequence domains: Ribosomal protein S13/S18
30S ribosomal protein S14 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
UniProt:
  • Canonical: A0A7U9IWF1 (Residues: 1-89; Coverage: 100%)
Gene names: G711_03755, rpsO
Sequence domains: Ribosomal protein S15
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
UniProt:
  • Canonical: A0A4P8C0R3 (Residues: 1-82; Coverage: 100%)
Gene names: CCU01_006955, rpsP
Sequence domains: Ribosomal protein S16
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
UniProt:
  • Canonical: F4VJV2 (Residues: 1-84; Coverage: 100%)
Gene names: ECPG_02631, rpsQ
Sequence domains: Ribosomal protein S17
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
UniProt:
  • Canonical: A0A1X3KX01 (Residues: 1-92; Coverage: 100%)
Gene names: EAVG_03054, rpsS
Sequence domains: Ribosomal protein S19
30S ribosomal protein S20 Chain: t
Molecule details ›
Chain: t
Length: 87 amino acids
Theoretical weight: 9.71 KDa
Source organism: Escherichia coli K-12
30S ribosomal protein S21 Chain: u
Molecule details ›
Chain: u
Length: 71 amino acids
Theoretical weight: 8.52 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
Sequence domains: Bacterial large subunit ribosomal RNA
5S ribosomal RNA Chain: B
Molecule details ›
Chain: B
Length: 120 nucleotides
Theoretical weight: 38.79 KDa
Sequence domains: 5S ribosomal RNA
16S ribosomal RNA Chain: a
Molecule details ›
Chain: a
Length: 1542 nucleotides
Theoretical weight: 499.87 KDa
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
Sequence domains: tRNA
P-site fMet-Phe-tRNA(Phe) Chain: w
Molecule details ›
Chain: w
Length: 76 nucleotides
Theoretical weight: 24.64 KDa
Sequence domains: tRNA
Messenger RNA Chain: z
Molecule details ›
Chain: z
Length: 33 nucleotides
Theoretical weight: 10.48 KDa

Ligands and Environments

2 bound ligands:
Ligand ZN 2 x ZN
Ligand AM2 1 x AM2
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: 9.5Å
Relevant EMDB volumes: EMD-13460

Quick links

Citations

3 review citations

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

1 mention without citation

Ratchet, swivel, tilt and roll: a complete description of subunit rotation in the ribosome.
Hassan et al. (2023)