› 6swd

Electron Microscopy
3.2Å resolution

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

Released:
DOI: 10.2210/pdb6swd/pdb
PDB entry 6swd coloured by chain, front view.
PDB entry 6swd coloured by chain, side view.
PDB entry 6swd 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
Commun Biol 3 58 (2020)
PMID: 32029867
Related structures: EMD-10323

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero nonadecamer (preferred)
PDBe Complex ID:
PDB-CPX-124656 (preferred)
Entry contents:
17 distinct polypeptide molecules
2 distinct RNA molecules
Macromolecules (19 distinct):
Small ribosomal subunit protein eS1 Chain: A
Molecule details ›
Chain: A
Length: 199 amino acids
Theoretical weight: 22.89 KDa
Source organism: Pyrococcus abyssi GE5
UniProt:
  • Canonical: Q9V2K7 (Residues: 1-199; Coverage: 100%)
Gene names: PAB0035, PYRAB00680, rps3ae
Sequence domains: Ribosomal S3Ae family
Small ribosomal subunit protein uS2 Chain: B
Molecule details ›
Chain: B
Length: 202 amino acids
Theoretical weight: 23.03 KDa
Source organism: Pyrococcus abyssi GE5
UniProt:
  • Canonical: Q9V191 (Residues: 1-202; Coverage: 100%)
Gene names: PAB0368, PYRAB05370, rps2
Sequence domains: Ribosomal protein S2
Small zinc finger protein HVO-2753-like zinc-binding pocket domain-containing protein Chain: C
Molecule details ›
Chain: C
Length: 63 amino acids
Theoretical weight: 7.16 KDa
Source organism: Pyrococcus abyssi GE5
UniProt:
  • Canonical: G8ZFK7 (Residues: 1-63; Coverage: 100%)
Gene name: PABs13722
Sequence domains: Small zinc finger protein HVO_2753-like, Zn-binding pocket
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: 28.25 KDa
Source organism: Pyrococcus abyssi GE5
UniProt:
  • Canonical: Q9V1U8 (Residues: 1-243; Coverage: 100%)
Gene names: PAB2397, PYRAB03290, rps4e
Sequence domains:
Small ribosomal subunit protein uS5 Chain: F
Molecule details ›
Chain: F
Length: 236 amino acids
Theoretical weight: 26.52 KDa
Source organism: Pyrococcus abyssi GE5
UniProt:
  • Canonical: Q9V1V5 (Residues: 1-236; Coverage: 100%)
Gene names: PAB2136, PYRAB03210, rps5
Sequence domains:
Small ribosomal subunit protein eS6 Chain: G
Molecule details ›
Chain: G
Length: 125 amino acids
Theoretical weight: 14.03 KDa
Source organism: Pyrococcus abyssi GE5
UniProt:
  • Canonical: Q9UYS3 (Residues: 1-125; Coverage: 100%)
Gene names: PAB1427, PYRAB14340, rps6e
Sequence domains: Ribosomal protein S6e
Small ribosomal subunit protein uS8 Chain: I
Molecule details ›
Chain: I
Length: 130 amino acids
Theoretical weight: 14.77 KDa
Source organism: Pyrococcus abyssi GE5
UniProt:
  • Canonical: Q9V1V0 (Residues: 1-130; Coverage: 100%)
Gene names: PAB2131, PYRAB03260, 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: Q9UZL4 (Residues: 1-127; Coverage: 100%)
Gene names: PAB0749, PYRAB11320, rps8e
Sequence domains: Ribosomal protein S8e
Small ribosomal subunit protein uS11 Chain: M
Molecule details ›
Chain: M
Length: 137 amino acids
Theoretical weight: 14.77 KDa
Source organism: Pyrococcus abyssi GE5
UniProt:
  • Canonical: P62010 (Residues: 1-137; Coverage: 100%)
Gene names: PAB0362, PYRAB05290, 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: 18.7 KDa
Source organism: Pyrococcus abyssi GE5
UniProt:
  • Canonical: Q9V2K9 (Residues: 1-158; Coverage: 100%)
Gene names: PAB0033, PYRAB00660, rps15
Sequence domains:
Small ribosomal subunit protein uS17 Chain: R
Molecule details ›
Chain: R
Length: 113 amino acids
Theoretical weight: 13.36 KDa
Source organism: Pyrococcus abyssi GE5
UniProt:
  • Canonical: Q9V1U5 (Residues: 1-113; Coverage: 100%)
Gene names: PAB2127, PYRAB03320, rps17
Sequence domains: Ribosomal protein S17
Small ribosomal subunit protein eS24 Chain: V
Molecule details ›
Chain: V
Length: 99 amino acids
Theoretical weight: 11.8 KDa
Source organism: Pyrococcus abyssi GE5
UniProt:
  • Canonical: Q9UY20 (Residues: 1-99; Coverage: 100%)
Gene names: PAB3419, PYRAB16880, rps24e
Sequence domains: Ribosomal protein S24e
Small ribosomal subunit protein eS27 Chain: W
Molecule details ›
Chain: W
Length: 65 amino acids
Theoretical weight: 7.19 KDa
Source organism: Pyrococcus abyssi GE5
UniProt:
  • Canonical: Q9UXZ3 (Residues: 1-65; Coverage: 100%)
Gene names: PAB7435, PYRAB17140, rps27e
Sequence domains: Ribosomal protein S27
Small ribosomal subunit protein eS32 Chain: 0
Molecule details ›
Chain: 0
Length: 36 amino acids
Theoretical weight: 4.91 KDa
Source organism: Pyrococcus abyssi GE5
UniProt:
  • Canonical: Q8U232 (Residues: 1-36; Coverage: 97%)
Gene names: PF1018, rpl41e
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: 1044 nucleotides
Theoretical weight: 340.43 KDa
Sequence domains: Archaeal small subunit ribosomal RNA
Messenger RNA Chain: 5
Molecule details ›
Chain: 5
Length: 20 nucleotides
Theoretical weight: 6.45 KDa

Ligands and Environments

2 bound ligands:
Ligand MG 25 x MG
Ligand ZN 5 x ZN
7 modified residues:
Ligand LHH 1 x LHH
Ligand A2M 1 x A2M
Ligand OMC 1 x OMC
Ligand 5HM 1 x 5HM
Ligand UR3 1 x UR3
Ligand 6MZ 1 x 6MZ
Ligand MA6 2 x MA6

Experiments and Validation Details

Entry percentile scores
Resolution: 3.2Å
Relevant EMDB volumes: EMD-10323
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)