› 7zag

Electron Microscopy
2.77Å resolution

Cryo-EM structure of a Pyrococcus abyssi 30S bound to Met-initiator tRNA,mRNA, aIF1A and the C-terminal domain of aIF5B.

Released:
DOI: 10.2210/pdb7zag/pdb
PDB entry 7zag coloured by chain, front view.
PDB entry 7zag coloured by chain, side view.
PDB entry 7zag coloured by chain, top view.
Source organism: Pyrococcus abyssi GE5
Primary publication:
Role of aIF5B in archaeal translation initiation.
Kazan R, Bourgeois G, Lazennec-Schurdevin C, Larquet E, Mechulam Y, Coureux PD, Schmitt E
Nucleic Acids Res (2022)
PMID: 35694843
Related structures: EMD-14579

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero 33-mer (preferred)
PDBe Complex ID:
PDB-CPX-124652 (preferred)
Entry contents:
30 distinct polypeptide molecules
3 distinct RNA molecules
Macromolecules (33 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:
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 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 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 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 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 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 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 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 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 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:
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
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: 134 amino acids
Theoretical weight: 15.34 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
Probable translation initiation factor IF-2, 2nd part Chain: 7
Molecule details ›
Chain: 7
Length: 619 amino acids
Theoretical weight: 69.12 KDa
Source organism: Pyrococcus abyssi GE5
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9UZK7 (Residues: 414-992; Coverage: 58%)
Gene names: PAB0755, PYRAB11390, infB
Sequence domains:
rRNA Chain: 2
Molecule details ›
Chain: 2
Length: 1497 nucleotides
Theoretical weight: 487.99 KDa
Sequence domains: Archaeal small subunit ribosomal RNA
Messenger RNA Chain: 5
Molecule details ›
Chain: 5
Length: 25 nucleotides
Theoretical weight: 8.06 KDa
Met-tRNAiMET Chain: 4
Molecule details ›
Chain: 4
Length: 77 nucleotides
Theoretical weight: 24.83 KDa
Sequence domains: tRNA

Ligands and Environments

3 bound ligands:
Ligand MG 62 x MG
Ligand ZN 6 x ZN
Ligand MET 1 x MET
14 modified residues:
Ligand OMU 7 x OMU
Ligand OMC 7 x OMC
Ligand LHH 2 x LHH
Ligand A2M 1 x A2M
Ligand OMG 9 x OMG
Ligand 5MC 9 x 5MC
Ligand B8H 1 x B8H
Ligand UR3 1 x UR3
Ligand 6MZ 1 x 6MZ
Ligand MA6 2 x MA6
Ligand 4SU 1 x 4SU
Ligand H2U 1 x H2U
Ligand 5MU 1 x 5MU
Ligand PSU 1 x PSU

Experiments and Validation Details

Entry percentile scores
Resolution: 2.77Å
Relevant EMDB volumes: EMD-14579
Expression system: Escherichia coli

Quick links

Citations

1 review citation

The molecular basis of translation initiation and its regulation in eukaryotes.
Brito Querido et al. (2024)
3 other articles

1 mention without citation

Role of aIF5B in archaeal translation initiation.
Kazan et al. (2022)