› 6fnn

X-ray diffraction
1.85Å resolution

Caldiarchaeum Subterraneum Ubiquitin:Rpn11-homolog complex

Released:
DOI: 10.2210/pdb6fnn/pdb
PDB entry 6fnn coloured by chain, front view.
PDB entry 6fnn coloured by chain, side view.
PDB entry 6fnn coloured by chain, top view.
Source organism: Candidatus Caldarchaeum subterraneum
Primary publication:
Rpn11-mediated ubiquitin processing in an ancestral archaeal ubiquitination system.
Fuchs ACD, Maldoner L, Wojtynek M, Hartmann MD, Martin J
Nat Commun 9 2696 (2018)
PMID: 30002364

Function and Biology Details

Reaction catalysed: 
Thiol-dependent hydrolysis of ester, thioester, amide, peptide and isopeptide bonds formed by the C-terminal Gly of ubiquitin (a 76-residue protein attached to proteins as an intracellular targeting signal).
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
MPN domain-containing protein Chains: A, B
Molecule details ›
Chains: A, B
Length: 155 amino acids
Theoretical weight: 17.06 KDa
Source organism: Candidatus Caldarchaeum subterraneum
Expression system: Escherichia coli
UniProt:
  • Canonical: E6N8B9 (Residues: 2-148; Coverage: 73%)
Gene names: CSUB_C1473, HGMM_F04B03C04, HGMM_F21D07C20, HGMM_F30C12C32
Sequence domains: JAB1/Mov34/MPN/PAD-1 ubiquitin protease
Ubiquitin-like domain-containing protein Chains: C, D
Molecule details ›
Chains: C, D
Length: 104 amino acids
Theoretical weight: 11.37 KDa
Source organism: Candidatus Caldarchaeum subterraneum
Expression system: Escherichia coli
UniProt:
  • Canonical: E6N8B8 (Residues: 1-78; Coverage: 90%)
Gene names: CSUB_C1474, HGMM_F04B03C03, HGMM_F21D07C21, HGMM_F30C12C33
Sequence domains: Ubiquitin family

Ligands and Environments

2 bound ligands:
Ligand ZN 2 x ZN
Ligand SO4 2 x SO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X10SA
Spacegroup: C2221
Unit cell:
a: 84.674Å b: 94.571Å c: 170.855Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.174 0.173 0.201
Expression system: Escherichia coli

Quick links

Citations

2 review citations

Multidomain ribosomal protein trees and the planctobacterial origin of neomura (eukaryotes, archaebacteria).
Cavalier-Smith et al. (2020)
1 more

1 mention without citation

Rpn11-mediated ubiquitin processing in an ancestral archaeal ubiquitination system.
Fuchs et al. (2018)