› 6cfw

Electron Microscopy
3.7Å resolution

cryoEM structure of a respiratory membrane-bound hydrogenase

Released:
DOI: 10.2210/pdb6cfw/pdb
PDB entry 6cfw coloured by chain, front view.
PDB entry 6cfw coloured by chain, side view.
PDB entry 6cfw coloured by chain, top view.
Source organisms:
Primary publication:
Structure of an Ancient Respiratory System.
Yu H, Wu CH, Schut GJ, Haja DK, Zhao G, Peters JW, Adams MWW, Li H
Cell 173 1636-1649.e16 (2018)
PMID: 29754813
Related structures: EMD-7468

Function and Biology Details

Reaction catalysed: 
H(2) + 2 oxidized ferredoxin = 2 reduced ferredoxin + 2 H(+)
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero tetradecamer (preferred)
PDBe Complex ID:
PDB-CPX-125156 (preferred)
Entry contents:
14 distinct polypeptide molecules
Macromolecules (14 distinct):
Monovalent cation/H+ antiporter subunit D Chain: H
Molecule details ›
Chain: H
Length: 510 amino acids
Theoretical weight: 55.02 KDa
Source organism: Pyrococcus furiosus COM1
Expression system: Pyrococcus furiosus
UniProt:
  • Canonical: I6UQL5 (Residues: 1-510; Coverage: 100%)
Gene name: PFC_06375
Sequence domains:
Monovalent cation/H+ antiporter subunit C Chain: G
Molecule details ›
Chain: G
Length: 117 amino acids
Theoretical weight: 12.78 KDa
Source organism: Pyrococcus furiosus COM1
Expression system: Pyrococcus furiosus
UniProt:
  • Canonical: I6UZU1 (Residues: 1-117; Coverage: 100%)
Gene name: PFC_06370
Sequence domains: NADH-ubiquinone/plastoquinone oxidoreductase chain 4L
MrpA C-terminal/MbhD domain-containing protein Chain: D
Molecule details ›
Chain: D
Length: 96 amino acids
Theoretical weight: 10.42 KDa
Source organism: Pyrococcus furiosus DSM 3638
Expression system: Pyrococcus furiosus
UniProt:
  • Canonical: Q8U104 (Residues: 1-96; Coverage: 100%)
Gene name: PF1426
Sequence domains: MBH, subunit D
Hydrogenase Chain: I
Molecule details ›
Chain: I
Length: 115 amino acids
Theoretical weight: 13.06 KDa
Source organism: Pyrococcus furiosus COM1
Expression system: Pyrococcus furiosus
UniProt:
  • Canonical: I6U847 (Residues: 1-115; Coverage: 100%)
Gene name: PFC_06380
Mbh13 NADH dehydrogenase subunit Chain: M
Molecule details ›
Chain: M
Length: 321 amino acids
Theoretical weight: 35.41 KDa
Source organism: Pyrococcus furiosus COM1
Expression system: Pyrococcus furiosus
UniProt:
  • Canonical: I6UQM0 (Residues: 1-321; Coverage: 100%)
Gene name: PFC_06400
Sequence domains: NADH dehydrogenase
Na+/H+ antiporter MnhB subunit-related protein domain-containing protein Chain: F
Molecule details ›
Chain: F
Length: 148 amino acids
Theoretical weight: 15.53 KDa
Source organism: Pyrococcus furiosus COM1
Expression system: Pyrococcus furiosus
UniProt:
  • Canonical: I6TXN5 (Residues: 1-148; Coverage: 100%)
Gene name: PFC_06365
Sequence domains: Domain related to MnhB subunit of Na+/H+ antiporter
Monovalent cation/H+ antiporter subunit E Chain: A
Molecule details ›
Chain: A
Length: 167 amino acids
Theoretical weight: 18.75 KDa
Source organism: Pyrococcus furiosus COM1
Expression system: Pyrococcus furiosus
UniProt:
  • Canonical: I6TXN1 (Residues: 1-167; Coverage: 100%)
Gene name: PFC_06340
Sequence domains: Na+/H+ ion antiporter subunit
MrpA C-terminal/MbhE domain-containing protein Chain: E
Molecule details ›
Chain: E
Length: 99 amino acids
Theoretical weight: 11.15 KDa
Source organism: Pyrococcus furiosus COM1
Expression system: Pyrococcus furiosus
UniProt:
  • Canonical: I6V287 (Residues: 1-99; Coverage: 100%)
Gene name: PFC_06360
Sequence domains: MBH, subunit E
Monovalent cation/H+ antiporter subunit G Chain: C
Molecule details ›
Chain: C
Length: 124 amino acids
Theoretical weight: 13.52 KDa
Source organism: Pyrococcus furiosus COM1
Expression system: Pyrococcus furiosus
UniProt:
  • Canonical: I6UQL1 (Residues: 1-124; Coverage: 100%)
Gene name: PFC_06350
Sequence domains: Na+/H+ antiporter subunit
Monovalent cation/H+ antiporter subunit F Chain: B
Molecule details ›
Chain: B
Length: 84 amino acids
Theoretical weight: 9.06 KDa
Source organism: Pyrococcus furiosus COM1
Expression system: Pyrococcus furiosus
UniProt:
  • Canonical: I6UZT7 (Residues: 1-84; Coverage: 100%)
Gene name: PFC_06345
Sequence domains: Multiple resistance and pH regulation protein F (MrpF / PhaF)
Probable membrane-bound hydrogenase subunit mbhJ Chain: J
Molecule details ›
Chain: J
Length: 167 amino acids
Theoretical weight: 18.32 KDa
Source organism: Pyrococcus furiosus DSM 3638
Expression system: Pyrococcus furiosus
UniProt:
  • Canonical: Q8U0Z8 (Residues: 1-167; Coverage: 100%)
Gene names: PF1432, mbh10, mbhJ
Sequence domains: NADH ubiquinone oxidoreductase, 20 Kd subunit
Structure domains: Rossmann fold
Membrane-bound hydrogenase subunit beta Chain: K
Molecule details ›
Chain: K
Length: 173 amino acids
Theoretical weight: 20.21 KDa
Source organism: Pyrococcus furiosus DSM 3638
Expression system: Pyrococcus furiosus
UniProt:
  • Canonical: Q8U0Z7 (Residues: 1-173; Coverage: 100%)
Gene names: PF1433, mbh11, mbhK
Sequence domains: Respiratory-chain NADH dehydrogenase, 30 Kd subunit
Membrane-bound hydrogenase subunit alpha Chain: L
Molecule details ›
Chain: L
Length: 380 amino acids
Theoretical weight: 43.01 KDa
Source organism: Pyrococcus furiosus DSM 3638
Expression system: Pyrococcus furiosus
UniProt:
  • Canonical: Q8U0Z6 (Residues: 1-380; Coverage: 89%)
Gene names: PF1434, mbh12, mbhL
Sequence domains:
4Fe-4S ferredoxin-type domain-containing protein Chain: N
Molecule details ›
Chain: N
Length: 139 amino acids
Theoretical weight: 15.71 KDa
Source organism: Pyrococcus furiosus COM1
Expression system: Pyrococcus furiosus
UniProt:
  • Canonical: I6U851 (Residues: 1-139; Coverage: 100%)
Gene name: PFC_06405
Sequence domains: 4Fe-4S dicluster domain

Ligands and Environments

2 bound ligands:
Ligand SF4 3 x SF4
Ligand NFU 1 x NFU
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.7Å
Relevant EMDB volumes: EMD-7468
Expression system: Pyrococcus furiosus

Quick links

Citations

9 review citations

Electron Bifurcation: A Long-Hidden Energy-Coupling Mechanism.
Müller et al. (2018)
8 more

10 mentions without citation

Evolution of complex I-like respiratory complexes.
Yu et al. (2021)
9 more