› 6tmf

Electron Microscopy
2.8Å resolution

Structure of an archaeal ABCE1-bound ribosomal post-splitting complex

Released:
DOI: 10.2210/pdb6tmf/pdb
PDB entry 6tmf coloured by chain, front view.
PDB entry 6tmf coloured by chain, side view.
PDB entry 6tmf coloured by chain, top view.
Source organisms:
Primary publication:
Molecular analysis of the ribosome recycling factor ABCE1 bound to the 30S post-splitting complex.
Nürenberg-Goloub E, Kratzat H, Heinemann H, Heuer A, Kötter P, Berninghausen O, Becker T, Tampé R, Beckmann R
EMBO J 39 e103788 (2020)
PMID: 32064661
Related structures: EMD-10519

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero 30-mer (preferred)
PDBe Complex ID:
PDB-CPX-215574 (preferred)
Entry contents:
29 distinct polypeptide molecules
1 distinct RNA molecule
Macromolecules (30 distinct):
Small ribosomal subunit protein uS2 Chain: B
Molecule details ›
Chain: B
Length: 195 amino acids
Theoretical weight: 22.3 KDa
Source organism: Thermococcus celer Vu 13 = JCM 8558
UniProt:
  • Canonical: A0A218NZR2 (Residues: 4-198; Coverage: 97%)
Gene names: A3L02_00670, rps2
Sequence domains: Ribosomal protein S2
Small ribosomal subunit protein uS3 Chain: C
Molecule details ›
Chain: C
Length: 193 amino acids
Theoretical weight: 21.71 KDa
Source organism: Thermococcus celer Vu 13 = JCM 8558
UniProt:
  • Canonical: A0A218NZU7 (Residues: 1-193; Coverage: 92%)
Gene names: A3L02_00870, rps3
Sequence domains:
Small ribosomal subunit protein eS1 Chain: D
Molecule details ›
Chain: D
Length: 184 amino acids
Theoretical weight: 21.59 KDa
Source organism: Thermococcus celer Vu 13 = JCM 8558
UniProt:
  • Canonical: A0A218P0R0 (Residues: 15-198; Coverage: 92%)
Gene names: A3L02_02445, rps3ae
Sequence domains: Ribosomal S3Ae family
Small ribosomal subunit protein uS4 Chain: E
Molecule details ›
Chain: E
Length: 178 amino acids
Theoretical weight: 20.98 KDa
Source organism: Thermococcus celer Vu 13 = JCM 8558
UniProt:
  • Canonical: A0A218NZV3 (Residues: 3-180; Coverage: 99%)
Gene names: A3L02_00725, rps4
Sequence domains: S4 domain
Small ribosomal subunit protein eS4 Chain: F
Molecule details ›
Chain: F
Length: 241 amino acids
Theoretical weight: 27.85 KDa
Source organism: Thermococcus celer Vu 13 = JCM 8558
UniProt:
  • Canonical: A0A218NZX1 (Residues: 3-243; Coverage: 99%)
Gene names: A3L02_00835, rps4e
Sequence domains:
Small ribosomal subunit protein uS5 Chain: G
Molecule details ›
Chain: G
Length: 220 amino acids
Theoretical weight: 24.54 KDa
Source organism: Thermococcus celer Vu 13 = JCM 8558
UniProt:
  • Canonical: A0A218P4N5 (Residues: 2-221; Coverage: 96%)
Gene names: A3L02_00795, rps5
Sequence domains:
Small ribosomal subunit protein eS6 Chain: H
Molecule details ›
Chain: H
Length: 125 amino acids
Theoretical weight: 13.83 KDa
Source organism: Thermococcus celer Vu 13 = JCM 8558
UniProt:
  • Canonical: A0A218P2W6 (Residues: 1-125; Coverage: 100%)
Gene names: A3L02_06645, rps6e
Sequence domains: Ribosomal protein S6e
Small ribosomal subunit protein uS7 Chain: I
Molecule details ›
Chain: I
Length: 214 amino acids
Theoretical weight: 24.29 KDa
Source organism: Thermococcus celer Vu 13 = JCM 8558
UniProt:
  • Canonical: A0A218P4K4 (Residues: 2-215; Coverage: 100%)
Gene names: A3L02_09870, rps7
Sequence domains: Ribosomal protein S7p/S5e
Small ribosomal subunit protein uS8 Chain: J
Molecule details ›
Chain: J
Length: 129 amino acids
Theoretical weight: 14.49 KDa
Source organism: Thermococcus celer Vu 13 = JCM 8558
UniProt:
  • Canonical: A0A218NZT7 (Residues: 2-130; Coverage: 99%)
Gene names: A3L02_00820, rps8
Sequence domains: Ribosomal protein S8
Small ribosomal subunit protein eS8 Chain: K
Molecule details ›
Chain: K
Length: 126 amino acids
Theoretical weight: 14.16 KDa
Source organism: Thermococcus celer Vu 13 = JCM 8558
UniProt:
  • Canonical: A0A218P4F6 (Residues: 2-127; Coverage: 97%)
Gene names: A3L02_09610, rps8e
Sequence domains: Ribosomal protein S8e
Small ribosomal subunit protein uS9 Chain: L
Molecule details ›
Chain: L
Length: 132 amino acids
Theoretical weight: 14.89 KDa
Source organism: Thermococcus celer Vu 13 = JCM 8558
UniProt:
  • Canonical: A0A218NZS6 (Residues: 1-132; Coverage: 98%)
Gene names: A3L02_00695, rps9
Sequence domains: Ribosomal protein S9/S16
Small ribosomal subunit protein uS10 Chain: M
Molecule details ›
Chain: M
Length: 102 amino acids
Theoretical weight: 11.73 KDa
Source organism: Thermococcus celer Vu 13 = JCM 8558
UniProt:
  • Canonical: A0A218P3Q8 (Residues: 1-102; Coverage: 100%)
Gene names: A3L02_08320, rps10, rps10p
Sequence domains: Ribosomal protein S10p/S20e
Small ribosomal subunit protein uS11 Chain: N
Molecule details ›
Chain: N
Length: 133 amino acids
Theoretical weight: 14.31 KDa
Source organism: Thermococcus celer Vu 13 = JCM 8558
UniProt:
  • Canonical: A0A218NZU0 (Residues: 7-139; Coverage: 96%)
Gene names: A3L02_00720, rps11
Sequence domains: Ribosomal protein S11
Small ribosomal subunit protein uS12 Chain: O
Molecule details ›
Chain: O
Length: 144 amino acids
Theoretical weight: 16.1 KDa
Source organism: Thermococcus celer Vu 13 = JCM 8558
UniProt:
  • Canonical: A0A218P4I2 (Residues: 3-146; Coverage: 98%)
Gene names: A3L02_09875, rps12
Sequence domains: Ribosomal protein S12/S23
Small ribosomal subunit protein uS13 Chain: P
Molecule details ›
Chain: P
Length: 136 amino acids
Theoretical weight: 15.77 KDa
Source organism: Thermococcus celer Vu 13 = JCM 8558
UniProt:
  • Canonical: A0A218NZT2 (Residues: 3-138; Coverage: 91%)
Gene names: A3L02_00730, rps13
Sequence domains: Ribosomal protein S13/S18
Small ribosomal subunit protein uS14 Chain: Q
Molecule details ›
Chain: Q
Length: 56 amino acids
Theoretical weight: 6.59 KDa
Source organism: Thermococcus celer Vu 13 = JCM 8558
UniProt:
  • Canonical: A0A218NZW1 (Residues: 1-56; Coverage: 100%)
Gene names: A3L02_00825, rps14, rps14P
Sequence domains: Ribosomal protein S14p/S29e
Small ribosomal subunit protein uS15 Chain: R
Molecule details ›
Chain: R
Length: 151 amino acids
Theoretical weight: 17.48 KDa
Source organism: Thermococcus celer Vu 13 = JCM 8558
UniProt:
  • Canonical: A0A218P0Q1 (Residues: 1-151; Coverage: 100%)
Gene names: A3L02_02460, rps15
Sequence domains:
Small ribosomal subunit protein uS17 Chain: S
Molecule details ›
Chain: S
Length: 111 amino acids
Theoretical weight: 13 KDa
Source organism: Thermococcus celer Vu 13 = JCM 8558
UniProt:
  • Canonical: A0A218NZX3 (Residues: 1-111; Coverage: 100%)
Gene names: A3L02_00850, rps17
Sequence domains: Ribosomal protein S17
Small ribosomal subunit protein eS17 Chain: T
Molecule details ›
Chain: T
Length: 64 amino acids
Theoretical weight: 7.72 KDa
Source organism: Thermococcus celer Vu 13 = JCM 8558
UniProt:
  • Canonical: A0A218P2C1 (Residues: 1-64; Coverage: 96%)
Gene names: A3L02_05615, rps17e
Sequence domains: Ribosomal S17
Small ribosomal subunit protein uS19 Chain: U
Molecule details ›
Chain: U
Length: 115 amino acids
Theoretical weight: 13.51 KDa
Source organism: Thermococcus celer Vu 13 = JCM 8558
UniProt:
  • Canonical: A0A218P4M9 (Residues: 6-120; Coverage: 87%)
Gene names: A3L02_00880, rps19p
Sequence domains: Ribosomal protein S19
Small ribosomal subunit protein eS19 Chain: V
Molecule details ›
Chain: V
Length: 149 amino acids
Theoretical weight: 17.2 KDa
Source organism: Thermococcus celer Vu 13 = JCM 8558
UniProt:
  • Canonical: A0A218P4W7 (Residues: 2-150; Coverage: 99%)
Gene names: A3L02_08625, rps19e
Sequence domains: Ribosomal protein S19e
Small zinc finger protein HVO-2753-like zinc-binding pocket domain-containing protein Chain: W
Molecule details ›
Chain: W
Length: 56 amino acids
Theoretical weight: 6.29 KDa
Source organism: Thermococcus celer Vu 13 = JCM 8558
UniProt:
  • Canonical: A0A218P055 (Residues: 4-59; Coverage: 95%)
Gene name: A3L02_01275
Sequence domains: Small zinc finger protein HVO_2753-like, Zn-binding pocket
Small ribosomal subunit protein eS24 Chain: X
Molecule details ›
Chain: X
Length: 97 amino acids
Theoretical weight: 11.41 KDa
Source organism: Thermococcus celer Vu 13 = JCM 8558
UniProt:
  • Canonical: A0A218P0B9 (Residues: 1-97; Coverage: 99%)
Gene names: A3L02_01605, rps24e
Sequence domains: Ribosomal protein S24e
Small ribosomal subunit protein eS27 Chain: Y
Molecule details ›
Chain: Y
Length: 63 amino acids
Theoretical weight: 6.84 KDa
Source organism: Thermococcus celer Vu 13 = JCM 8558
UniProt:
  • Canonical: A0A218NZS1 (Residues: 3-65; Coverage: 97%)
Gene names: A3L02_00590, rps27e
Sequence domains: Ribosomal protein S27
Small ribosomal subunit protein eS31 Chain: Z
Molecule details ›
Chain: Z
Length: 50 amino acids
Theoretical weight: 6 KDa
Source organism: Thermococcus celer Vu 13 = JCM 8558
UniProt:
  • Canonical: A0A218P0A5 (Residues: 1-50; Coverage: 98%)
Gene names: A3L02_01600, rps27ae
Sequence domains: Ribosomal protein S27a
Small ribosomal subunit protein eS28 Chain: a
Molecule details ›
Chain: a
Length: 66 amino acids
Theoretical weight: 7.36 KDa
Source organism: Thermococcus celer Vu 13 = JCM 8558
UniProt:
  • Canonical: A0A218P147 (Residues: 1-66; Coverage: 94%)
Gene names: A3L02_03310, rps28e
Sequence domains: Ribosomal protein S28e
Large ribosomal subunit protein eL8 Chain: b
Molecule details ›
Chain: b
Length: 123 amino acids
Theoretical weight: 13.35 KDa
Source organism: Thermococcus celer Vu 13 = JCM 8558
UniProt:
  • Canonical: A0A218P167 (Residues: 1-123; Coverage: 100%)
Gene names: A3L02_03315, rpl7ae
Sequence domains: Ribosomal protein L7Ae/L30e/S12e/Gadd45 family
LSU ribosomal protein L41E Chain: c
Molecule details ›
Chain: c
Length: 37 amino acids
Theoretical weight: 5.02 KDa
Source organism: Thermococcus celer Vu 13 = JCM 8558
UniProt:
  • Canonical: A0A218P2S9 (Residues: 1-37; Coverage: 100%)
Gene name: A3L02_06520
RNase L inhibitor Chain: d
Molecule details ›
Chain: d
Length: 594 amino acids
Theoretical weight: 67.2 KDa
Source organism: Saccharolobus solfataricus
Expression system: Escherichia coli
UniProt:
  • Canonical: Q980K5 (Residues: 1-594; Coverage: 99%)
Gene name: SSO0287
Sequence domains:
16S ribosomal RNA Chain: A
Molecule details ›
Chain: A
Length: 1485 nucleotides
Theoretical weight: 482.21 KDa
Sequence domains: Archaeal small subunit ribosomal RNA

Ligands and Environments

4 bound ligands:
Ligand MG 29 x MG
Ligand ZN 4 x ZN
Ligand SF4 2 x SF4
Ligand ANP 2 x ANP
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 2.8Å
Relevant EMDB volumes: EMD-10519
Expression system: Escherichia coli

Quick links

Citations

10 review citations

Ribosomal stress-surveillance: three pathways is a magic number.
Vind et al. (2020)
9 more

4 mentions without citation

Molecular analysis of the ribosome recycling factor ABCE1 bound to the 30S post-splitting complex.
Nürenberg-Goloub et al. (2020)
3 more