› 5zbu

X-ray diffraction
3.2Å resolution

Crystal Structure of PA-TM-RING E3 ligase RNF13 RING domain in complex with E2~Ub

Released:
DOI: 10.2210/pdb5zbu/pdb
PDB entry 5zbu coloured by chain, front view.
PDB entry 5zbu coloured by chain, side view.
PDB entry 5zbu coloured by chain, top view.
Source organism: Homo sapiens
Entry authors: Datta AB, Sarkar S

Function and Biology Details

Reactions catalysed: 
S-ubiquitinyl-[E1 ubiquitin-activating enzyme]-L-cysteine + [E2 ubiquitin-conjugating enzyme]-L-cysteine = [E1 ubiquitin-activating enzyme]-L-cysteine + S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine
(1a) S-ubiquitinyl-[E1 ubiquitin-activating enzyme]-L-cysteine + [(E3-independent) E2 ubiquitin-conjugating enzyme]-L-cysteine = [E1 ubiquitin-activating enzyme]-L-cysteine + S-monoubiquitinyl-[(E3-independent) ubiquitin-conjugating enzyme]-L-cysteine
S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine + [acceptor protein]-L-lysine = [E2 ubiquitin-conjugating enzyme]-L-cysteine + N(6)-ubiquitinyl-[acceptor protein]-L-lysine
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assemblies composition:
hetero dimer
hetero trimer (preferred)
PDBe Complex ID:
PDB-CPX-129001 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Ubiquitin-conjugating enzyme E2 D2 Chains: B, C
Molecule details ›
Chains: B, C
Length: 148 amino acids
Theoretical weight: 16.84 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P62837 (Residues: 1-147; Coverage: 100%)
Gene names: PUBC1, UBC4, UBC5B, UBCH4, UBCH5B, UBE2D2
Sequence domains: Ubiquitin-conjugating enzyme
E3 ubiquitin-protein ligase RNF13 Chains: A, D
Molecule details ›
Chains: A, D
Length: 76 amino acids
Theoretical weight: 8.84 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: O43567 (Residues: 216-290; Coverage: 22%)
Gene names: RNF13, RZF
Sequence domains: Ring finger domain
Ubiquitin Chain: E
Molecule details ›
Chain: E
Length: 76 amino acids
Theoretical weight: 8.58 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P0CG47 (Residues: 153-228; Coverage: 33%)
Gene name: UBB
Sequence domains: Ubiquitin family

Ligands and Environments

1 bound ligand:
Ligand ZN 4 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RRCAT INDUS-2 BEAMLINE PX-BL21
Spacegroup: P21
Unit cell:
a: 56.559Å b: 105.74Å c: 60.79Å
α: 90° β: 115.49° γ: 90°
R-values:
R R work R free
0.217 0.214 0.262
Expression system: Escherichia coli

Quick links