› 3vyt

X-ray diffraction
2.25Å resolution

Crystal structure of the HypC-HypD-HypE complex (form I inward)

Released:
DOI: 10.2210/pdb3vyt/pdb
PDB entry 3vyt coloured by chain, front view.
PDB entry 3vyt coloured by chain, side view.
PDB entry 3vyt coloured by chain, top view.
Source organism: Thermococcus kodakarensis KOD1
Primary publication:
Crystal structures of the HypCD complex and the HypCDE ternary complex: transient intermediate complexes during [NiFe] hydrogenase maturation.
Watanabe S, Matsumi R, Atomi H, Imanaka T, Miki K
Structure 20 2124-37 (2012)
PMID: 23123111

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero hexamer (preferred)
PDBe Complex ID:
PDB-CPX-177317 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Hydrogenase expression/formation protein HypC Chain: A
Molecule details ›
Chain: A
Length: 74 amino acids
Theoretical weight: 8.13 KDa
Source organism: Thermococcus kodakarensis KOD1
Expression system: Escherichia coli
UniProt:
  • Canonical: Q5JII0 (Residues: 2-75; Coverage: 99%)
Gene names: TK2001, Tk-hypC
Sequence domains: HupF/HypC family
Structure domains: SH3 type barrels.
hydrogenase expression/formation protein HypD Chain: B
Molecule details ›
Chain: B
Length: 372 amino acids
Theoretical weight: 41.93 KDa
Source organism: Thermococcus kodakarensis KOD1
Expression system: Escherichia coli
UniProt:
  • Canonical: Q5JII1 (Residues: 1-372; Coverage: 100%)
Gene names: TK2000, Tk-hypD
Sequence domains: Hydrogenase formation hypA family
Structure domains:
Hydrogenase expression/formation protein HypE Chain: C
Molecule details ›
Chain: C
Length: 338 amino acids
Theoretical weight: 35.95 KDa
Source organism: Thermococcus kodakarensis KOD1
Expression system: Escherichia coli
UniProt:
  • Canonical: Q5JII7 (Residues: 1-338; Coverage: 100%)
Gene name: TK1993
Sequence domains:
Structure domains:

Ligands and Environments

3 bound ligands:
Ligand SF4 1 x SF4
Ligand MG 5 x MG
Ligand CL 1 x CL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL41XU
Spacegroup: C2
Unit cell:
a: 78.333Å b: 99.412Å c: 103.923Å
α: 90° β: 97.79° γ: 90°
R-values:
R R work R free
0.207 0.207 0.253
Expression system: Escherichia coli

Quick links

Citations

15 citation in other articles

Structural basis of a Ni acquisition cycle for [NiFe] hydrogenase by Ni-metallochaperone HypA and its enhancer.
Watanabe et al. (2015)
14 more

3 mentions without citation

Modeling the assembly order of multimeric heteroprotein complexes.
Peterson et al. (2018)
2 more