› 5jbh

Electron Microscopy
5.34Å resolution

Cryo-EM structure of a full archaeal ribosomal translation initiation complex in the P-IN conformation

Released:
DOI: 10.2210/pdb5jbh/pdb
PDB entry 5jbh coloured by chain, front view.
PDB entry 5jbh coloured by chain, side view.
PDB entry 5jbh coloured by chain, top view.
Source organism: Pyrococcus abyssi GE5
Primary publication:
Cryo-EM study of start codon selection during archaeal translation initiation.
Coureux PD, Lazennec-Schurdevin C, Monestier A, Larquet E, Cladière L, Klaholz BP, Schmitt E, Mechulam Y
Nat Commun 7 13366 (2016)
PMID: 27819266
Related structures: EMD-8149

Function and Biology Details

Reaction catalysed: 
GTP + H(2)O = GDP + phosphate
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero 36-mer (preferred)
PDBe Complex ID:
PDB-CPX-158425 (preferred)
Entry contents:
33 distinct polypeptide molecules
3 distinct RNA molecules
Macromolecules (36 distinct):
Small ribosomal subunit protein uS3 Chain: Z
Molecule details ›
Chain: Z
Length: 210 amino acids
Theoretical weight: 23.46 KDa
Source organism: Pyrococcus abyssi GE5
UniProt:
  • Canonical: Q8U004 (Residues: 1-210; Coverage: 100%)
Gene names: PF1819, rps3
Sequence domains:
Large ribosomal subunit protein eL8 Chain: 3
Molecule details ›
Chain: 3
Length: 123 amino acids
Theoretical weight: 13.41 KDa
Source organism: Pyrococcus abyssi GE5
UniProt:
  • Canonical: P62008 (Residues: 1-123; Coverage: 100%)
Gene names: PAB0460, PYRAB06750, rpl7ae
Sequence domains: Ribosomal protein L7Ae/L30e/S12e/Gadd45 family
Small ribosomal subunit protein uS10 Chain: L
Molecule details ›
Chain: L
Length: 102 amino acids
Theoretical weight: 11.77 KDa
Source organism: Pyrococcus abyssi GE5
UniProt:
  • Canonical: P61885 (Residues: 1-102; Coverage: 100%)
Gene names: PF1376, rps10
Sequence domains: Ribosomal protein S10p/S20e
Small ribosomal subunit protein uS13 Chain: O
Molecule details ›
Chain: O
Length: 148 amino acids
Theoretical weight: 16.95 KDa
Source organism: Pyrococcus abyssi GE5
UniProt:
  • Canonical: Q8U0E2 (Residues: 1-148; Coverage: 100%)
Gene names: PF1650, rps13
Sequence domains: Ribosomal protein S13/S18
Small ribosomal subunit protein uS14 Chain: P
Molecule details ›
Chain: P
Length: 56 amino acids
Theoretical weight: 6.63 KDa
Source organism: Pyrococcus abyssi GE5
UniProt:
  • Canonical: Q8U013 (Residues: 1-56; Coverage: 100%)
Gene names: PF1810, rps14
Sequence domains: Ribosomal protein S14p/S29e
Small ribosomal subunit protein eS17 Chain: S
Molecule details ›
Chain: S
Length: 67 amino acids
Theoretical weight: 7.94 KDa
Source organism: Pyrococcus abyssi GE5
UniProt:
  • Canonical: Q8U0U1 (Residues: 1-67; Coverage: 100%)
Gene names: PF1491, rps17e
Sequence domains: Ribosomal S17
Small ribosomal subunit protein uS19 Chain: T
Molecule details ›
Chain: T
Length: 132 amino acids
Theoretical weight: 15.36 KDa
Source organism: Pyrococcus abyssi GE5
UniProt:
  • Canonical: Q8U002 (Residues: 1-132; Coverage: 100%)
Gene names: PF1821, rps19
Sequence domains: Ribosomal protein S19
Small ribosomal subunit protein eS19 Chain: U
Molecule details ›
Chain: U
Length: 150 amino acids
Theoretical weight: 17.39 KDa
Source organism: Pyrococcus abyssi GE5
UniProt:
  • Canonical: Q9V0G8 (Residues: 1-150; Coverage: 100%)
Gene names: PAB1813, PYRAB08210, rps19e
Sequence domains: Ribosomal protein S19e
Small ribosomal subunit protein eS28 Chain: X
Molecule details ›
Chain: X
Length: 71 amino acids
Theoretical weight: 8.12 KDa
Source organism: Pyrococcus abyssi GE5
UniProt:
  • Canonical: Q8U159 (Residues: 1-71; Coverage: 100%)
Gene names: PF1368, rps28e
Sequence domains: Ribosomal protein S28e
Small ribosomal subunit protein eS31 Chain: Y
Molecule details ›
Chain: Y
Length: 50 amino acids
Theoretical weight: 5.86 KDa
Source organism: Pyrococcus abyssi GE5
UniProt:
  • Canonical: Q8U443 (Residues: 1-50; Coverage: 100%)
Gene names: PF0252, rps27ae
Sequence domains: Ribosomal protein S27a
Small ribosomal subunit protein uS7 Chain: H
Molecule details ›
Chain: H
Length: 215 amino acids
Theoretical weight: 24.7 KDa
Source organism: Pyrococcus abyssi GE5
UniProt:
  • Canonical: Q8U0M8 (Residues: 1-215; Coverage: 100%)
Gene names: PF1558, rps7
Sequence domains: Ribosomal protein S7p/S5e
Small ribosomal subunit protein uS9 Chain: K
Molecule details ›
Chain: K
Length: 135 amino acids
Theoretical weight: 15.32 KDa
Source organism: Pyrococcus abyssi GE5
UniProt:
  • Canonical: Q8U0E7 (Residues: 1-135; Coverage: 100%)
Gene names: PF1644, rps9
Sequence domains: Ribosomal protein S9/S16
Small ribosomal subunit protein uS11 Chain: M
Molecule details ›
Chain: M
Length: 137 amino acids
Theoretical weight: 14.76 KDa
Source organism: Pyrococcus abyssi GE5
UniProt:
  • Canonical: Q8U0E3 (Residues: 1-137; Coverage: 100%)
Gene names: PF1648, rps11
Sequence domains: Ribosomal protein S11
Small ribosomal subunit protein uS12 Chain: N
Molecule details ›
Chain: N
Length: 147 amino acids
Theoretical weight: 16.48 KDa
Source organism: Pyrococcus abyssi GE5
UniProt:
  • Canonical: P61994 (Residues: 1-147; Coverage: 100%)
Gene names: PAB0427, PYRAB06190, rps12
Sequence domains: Ribosomal protein S12/S23
Small ribosomal subunit protein uS15 Chain: Q
Molecule details ›
Chain: Q
Length: 158 amino acids
Theoretical weight: 18.64 KDa
Source organism: Pyrococcus abyssi GE5
UniProt:
  • Canonical: Q8TZD9 (Residues: 1-158; Coverage: 100%)
Gene names: PF2056, rps15
Sequence domains:
Small ribosomal subunit protein uS17 Chain: R
Molecule details ›
Chain: R
Length: 113 amino acids
Theoretical weight: 13.3 KDa
Source organism: Pyrococcus abyssi GE5
UniProt:
  • Canonical: Q8U008 (Residues: 1-113; Coverage: 100%)
Gene names: PF1815, rps17
Sequence domains: Ribosomal protein S17
Small ribosomal subunit protein eS1 Chain: A
Molecule details ›
Chain: A
Length: 198 amino acids
Theoretical weight: 22.98 KDa
Source organism: Pyrococcus abyssi GE5
UniProt:
  • Canonical: Q8TZE1 (Residues: 1-198; Coverage: 100%)
Gene names: PF2054, rps3ae
Sequence domains: Ribosomal S3Ae family
Small ribosomal subunit protein uS2 Chain: B
Molecule details ›
Chain: B
Length: 202 amino acids
Theoretical weight: 23.04 KDa
Source organism: Pyrococcus abyssi GE5
UniProt:
  • Canonical: Q8U0F0 (Residues: 1-202; Coverage: 100%)
Gene names: PF1640, rps2
Sequence domains: Ribosomal protein S2
Small ribosomal subunit protein eS24 Chain: V
Molecule details ›
Chain: V
Length: 99 amino acids
Theoretical weight: 11.7 KDa
Source organism: Pyrococcus abyssi GE5
UniProt:
  • Canonical: Q8U442 (Residues: 1-99; Coverage: 100%)
Gene names: PF0253, rps24e
Sequence domains: Ribosomal protein S24e
Small ribosomal subunit protein eS27 Chain: W
Molecule details ›
Chain: W
Length: 63 amino acids
Theoretical weight: 6.89 KDa
Source organism: Pyrococcus abyssi GE5
UniProt:
  • Canonical: Q8U474 (Residues: 1-63; Coverage: 100%)
Gene names: PF0218, rps27e
Sequence domains: Ribosomal protein S27
Small ribosomal subunit protein uS4 Chain: D
Molecule details ›
Chain: D
Length: 180 amino acids
Theoretical weight: 21.38 KDa
Source organism: Pyrococcus abyssi GE5
UniProt:
  • Canonical: P61992 (Residues: 1-180; Coverage: 100%)
Gene names: PAB0361, PYRAB05280, rps4
Sequence domains: S4 domain
Small ribosomal subunit protein eS4 Chain: E
Molecule details ›
Chain: E
Length: 243 amino acids
Theoretical weight: 28.2 KDa
Source organism: Pyrococcus abyssi GE5
UniProt:
  • Canonical: Q8U011 (Residues: 1-243; Coverage: 100%)
Gene names: PF1812, rps4e
Sequence domains:
Small ribosomal subunit protein uS5 Chain: F
Molecule details ›
Chain: F
Length: 236 amino acids
Theoretical weight: 26.59 KDa
Source organism: Pyrococcus abyssi GE5
UniProt:
  • Canonical: Q8U017 (Residues: 1-236; Coverage: 100%)
Gene names: PF1804, rps5
Sequence domains:
Small ribosomal subunit protein eS6 Chain: G
Molecule details ›
Chain: G
Length: 125 amino acids
Theoretical weight: 14 KDa
Source organism: Pyrococcus abyssi GE5
UniProt:
  • Canonical: Q8U3H8 (Residues: 1-125; Coverage: 100%)
Gene names: PF0488, rps6e
Sequence domains: Ribosomal protein S6e
Small ribosomal subunit protein uS8 Chain: I
Molecule details ›
Chain: I
Length: 130 amino acids
Theoretical weight: 14.68 KDa
Source organism: Pyrococcus abyssi GE5
UniProt:
  • Canonical: Q8U014 (Residues: 1-130; Coverage: 100%)
Gene names: PF1809, rps8
Sequence domains: Ribosomal protein S8
Small ribosomal subunit protein eS8 Chain: J
Molecule details ›
Chain: J
Length: 127 amino acids
Theoretical weight: 14.29 KDa
Source organism: Pyrococcus abyssi GE5
UniProt:
  • Canonical: Q8U1Y5 (Residues: 1-127; Coverage: 100%)
Gene names: PF1069, rps8e
Sequence domains: Ribosomal protein S8e
30S ribosomal protein SX Chain: C
Molecule details ›
Chain: C
Length: 57 amino acids
Theoretical weight: 4.87 KDa
Source organism: Pyrococcus abyssi GE5
Small ribosomal subunit protein eS32 Chain: 0
Molecule details ›
Chain: 0
Length: 22 amino acids
Theoretical weight: 3.05 KDa
Source organism: Pyrococcus abyssi GE5
UniProt:
  • Canonical: Q8U232 (Residues: 14-35; Coverage: 60%)
Gene names: PF1018, rpl41e
Protein translation factor SUI1 homolog Chain: 1
Molecule details ›
Chain: 1
Length: 102 amino acids
Theoretical weight: 11.62 KDa
Source organism: Pyrococcus abyssi GE5
Expression system: Escherichia coli
UniProt:
  • Canonical: Q57902 (Residues: 2-103; Coverage: 99%)
Gene name: MJ0463
Sequence domains: Translation initiation factor SUI1
Translation initiation factor 1A Chain: 6
Molecule details ›
Chain: 6
Length: 113 amino acids
Theoretical weight: 13.08 KDa
Source organism: Pyrococcus abyssi GE5
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9V138 (Residues: 1-113; Coverage: 100%)
Gene names: PAB2441, PYRAB05910, aif1A, eIF1A
Sequence domains: Translation initiation factor 1A / IF-1
Translation initiation factor 2 subunit gamma Chain: 7
Molecule details ›
Chain: 7
Length: 415 amino acids
Theoretical weight: 45.85 KDa
Source organism: Pyrococcus abyssi GE5
Expression system: Escherichia coli
UniProt:
  • Canonical: Q980A5 (Residues: 1-415; Coverage: 100%)
Gene names: SSO0412, eif2g
Sequence domains:
Translation initiation factor 2 subunit beta Chain: 8
Molecule details ›
Chain: 8
Length: 139 amino acids
Theoretical weight: 15.94 KDa
Source organism: Pyrococcus abyssi GE5
Expression system: Escherichia coli
UniProt:
  • Canonical: Q97W59 (Residues: 1-139; Coverage: 100%)
Gene names: SSO2381, aif2b, eif2b
Sequence domains: Domain found in IF2B/IF5
Translation initiation factor 2 subunit alpha Chain: 9
Molecule details ›
Chain: 9
Length: 266 amino acids
Theoretical weight: 30.43 KDa
Source organism: Pyrococcus abyssi GE5
Expression system: Escherichia coli
UniProt:
  • Canonical: Q97Z79 (Residues: 1-266; Coverage: 100%)
Gene names: SSO1050, aif2a, eif2a
Sequence domains:
16S ribosomal RNA Chain: 2
Molecule details ›
Chain: 2
Length: 1518 nucleotides
Theoretical weight: 492.8 KDa
Sequence domains: Archaeal small subunit ribosomal RNA
Messenger RNA Chain: 5
Molecule details ›
Chain: 5
Length: 26 nucleotides
Theoretical weight: 8.39 KDa
initiator Met-tRNA fMet from E. coli (A1U72 variant) Chain: 4
Molecule details ›
Chain: 4
Length: 76 nucleotides
Theoretical weight: 24.49 KDa
Sequence domains: tRNA

Ligands and Environments

4 bound ligands:
Ligand MET 1 x MET
Ligand MG 1 x MG
Ligand GNP 1 x GNP
Ligand ZN 1 x ZN
3 modified residues:
Ligand H2U 1 x H2U
Ligand OMC 1 x OMC
Ligand 5MU 1 x 5MU

Experiments and Validation Details

Entry percentile scores
Resolution: 5.34Å
Relevant EMDB volumes: EMD-8149
Expression system: Escherichia coli

Quick links

Citations

5 review citations

Translation in Prokaryotes.
Rodnina MV. (2018)
4 more

2 mentions without citation

Cryo-EM study of start codon selection during archaeal translation initiation.
Coureux et al. (2016)
1 more