› 6swe

Electron Microscopy
3.1Å resolution

IC2 head of cryo-EM structure of a full archaeal ribosomal translation initiation complex devoid of aIF1 in P. abyssi

Released:
DOI: 10.2210/pdb6swe/pdb
PDB entry 6swe coloured by chain, front view.
PDB entry 6swe coloured by chain, side view.
PDB entry 6swe coloured by chain, top view.
Source organism: Pyrococcus abyssi GE5
Primary publication:
Cryo-EM study of an archaeal 30S initiation complex gives insights into evolution of translation initiation.
Coureux PD, Lazennec-Schurdevin C, Bourcier S, Mechulam Y, Schmitt E
OpenAccess logo Commun Biol 3 58 (2020)
PMID: 32029867
Related structures: EMD-10324

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero pentadecamer (preferred)
PDBe Complex ID:
PDB-CPX-158189 (preferred)
Entry contents:
13 distinct polypeptide molecules
2 distinct RNA molecules
Macromolecules (15 distinct):
Small ribosomal subunit protein uS7 Chain: H
Molecule details ›
Chain: H
Length: 215 amino acids
Theoretical weight: 24.66 KDa
Source organism: Pyrococcus abyssi GE5
UniProt:
  • Canonical: Q9V109 (Residues: 1-215; Coverage: 100%)
Gene names: PAB0428, PYRAB06200, rps7
Sequence domains: Ribosomal protein S7p/S5e
Small ribosomal subunit protein uS9 Chain: K
Molecule details ›
Chain: K
Length: 135 amino acids
Theoretical weight: 15.29 KDa
Source organism: Pyrococcus abyssi GE5
UniProt:
  • Canonical: Q9V195 (Residues: 1-135; Coverage: 100%)
Gene names: PAB0366, PYRAB05330, rps9
Sequence domains: Ribosomal protein S9/S16
Small ribosomal subunit protein uS10 Chain: L
Molecule details ›
Chain: L
Length: 102 amino acids
Theoretical weight: 11.8 KDa
Source organism: Pyrococcus abyssi GE5
UniProt:
  • Canonical: Q9V0V6 (Residues: 1-102; Coverage: 100%)
Gene names: PAB0466, PYRAB06840, rps10
Sequence domains: Ribosomal protein S10p/S20e
Small ribosomal subunit protein uS13 Chain: O
Molecule details ›
Chain: O
Length: 148 amino acids
Theoretical weight: 16.99 KDa
Source organism: Pyrococcus abyssi GE5
UniProt:
  • Canonical: Q9V1A0 (Residues: 1-148; Coverage: 100%)
Gene names: PAB0360, PYRAB05270, rps13
Sequence domains: Ribosomal protein S13/S18
Small ribosomal subunit protein uS14 Chain: P
Molecule details ›
Chain: P
Length: 56 amino acids
Theoretical weight: 6.64 KDa
Source organism: Pyrococcus abyssi GE5
UniProt:
  • Canonical: P62012 (Residues: 1-56; Coverage: 100%)
Gene names: PAB7080, PYRAB03270, rps14
Sequence domains: Ribosomal protein S14p/S29e
Small ribosomal subunit protein eS17 Chain: S
Molecule details ›
Chain: S
Length: 67 amino acids
Theoretical weight: 8.06 KDa
Source organism: Pyrococcus abyssi GE5
UniProt:
  • Canonical: Q9V0G0 (Residues: 1-67; Coverage: 100%)
Gene names: PAB7207, PYRAB08290, rps17e
Sequence domains: Ribosomal S17
Small ribosomal subunit protein uS19 Chain: T
Molecule details ›
Chain: T
Length: 132 amino acids
Theoretical weight: 15.31 KDa
Source organism: Pyrococcus abyssi GE5
UniProt:
  • Canonical: Q9V1T9 (Residues: 1-132; Coverage: 100%)
Gene names: PAB2123, PYRAB03380, rps19
Sequence domains: Ribosomal protein S19
Small ribosomal subunit protein eS19 Chain: U
Molecule details ›
Chain: U
Length: 150 amino acids
Theoretical weight: 17.42 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: 8.1 KDa
Source organism: Pyrococcus abyssi GE5
UniProt:
  • Canonical: P61029 (Residues: 1-71; Coverage: 100%)
Gene names: PAB7165, PYRAB06760, rps28e
Sequence domains: Ribosomal protein S28e
Small ribosomal subunit protein eS31 Chain: Y
Molecule details ›
Chain: Y
Length: 51 amino acids
Theoretical weight: 5.99 KDa
Source organism: Pyrococcus abyssi GE5
UniProt:
  • Canonical: P61238 (Residues: 1-51; Coverage: 100%)
Gene names: PAB3419a, PYRAB16885, rps27ae
Sequence domains: Ribosomal protein S27a
Small ribosomal subunit protein uS3 Chain: Z
Molecule details ›
Chain: Z
Length: 210 amino acids
Theoretical weight: 23.47 KDa
Source organism: Pyrococcus abyssi GE5
UniProt:
  • Canonical: Q9V1U1 (Residues: 1-210; Coverage: 100%)
Gene names: PAB2125, PYRAB03360, rps3
Sequence domains:
Large ribosomal subunit protein eL8 Chain: 3
Molecule details ›
Chain: 3
Length: 123 amino acids
Theoretical weight: 13.44 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
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
16S ribosomal RNA Chain: 2
Molecule details ›
Chain: 2
Length: 468 nucleotides
Theoretical weight: 152.07 KDa
Sequence domains: Archaeal small subunit ribosomal RNA
initiator Met-tRNA fMet from E. coli (A1U72 variant) Chain: 4
Molecule details ›
Chain: 4
Length: 18 nucleotides
Theoretical weight: 5.76 KDa

Ligands and Environments

2 bound ligands:
Ligand MG 8 x MG
Ligand ZN 1 x ZN
3 modified residues:
Ligand B8H 1 x B8H
Ligand 5MC 2 x 5MC
Ligand OMC 1 x OMC

Experiments and Validation Details

Entry percentile scores
Resolution: 3.1Å
Relevant EMDB volumes: EMD-10324
Expression system: Escherichia coli

Quick links

Citations

5 review citations

Ribosome Biogenesis in Archaea.
Londei et al. (2021)
4 more

1 mention without citation

Cryo-EM study of an archaeal 30S initiation complex gives insights into evolution of translation initiation.
Coureux et al. (2020)