6CFW | pdb_00006cfw

cryoEM structure of a respiratory membrane-bound hydrogenase

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Membrane Protein Annotation: OPM
Membrane Protein Annotation: PDBTM
Membrane Protein Annotation: MemProtMD
Membrane Protein Annotation: mpstruc

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B [auth G]	SCOP2 Family	NADH-quinone oxidoreductase NDH subunit 11-like	8093352	4005793	SCOP2 (2022-06-29)
B [auth G]	SCOP2 Superfamily	NADH-quinone oxidoreductase, subunit 11-like	8093353	3002200	SCOP2 (2022-06-29)
C [auth D]	SCOP2 Family	NADH-quinone oxidoreductase NDH subunit 10-like	8093354	4005844	SCOP2 (2022-06-29)
C [auth D]	SCOP2 Superfamily	NADH-quinone oxidoreductase, subunit 11-like	8093355	3002200	SCOP2 (2022-06-29)
E [auth M]	SCOP2 Family	NADH-quinone oxidoreductase subunit 8-like	8067554	4005664	SCOP2 (2022-06-29)
E [auth M]	SCOP2 Superfamily	Antiporter subunits half-channel-like	8067555	3002280	SCOP2 (2022-06-29)
I [auth C]	SCOP2 Family	Monovalent cation/H+ antiporter MBH, subunit G	8093343	4007805	SCOP2 (2022-06-29)
I [auth C]	SCOP2 Superfamily	NADH-quinone oxidoreductase, subunit 11-like	8093344	3002200	SCOP2 (2022-06-29)
J [auth B]	SCOP2 Family	Monovalent cation/H+ antiporter MBH, subunit F	8093341	4007804	SCOP2 (2022-06-29)
J [auth B]	SCOP2 Superfamily	NADH-quinone oxidoreductase, subunit 11-like	8093342	3002200	SCOP2 (2022-06-29)
K [auth J]	SCOP2 Family	Nq06/HydA N-terminal domain-like	8085730	4007641	SCOP2 (2022-06-29)
K [auth J]	SCOP2 Superfamily	Nqo6/HydA N-terminal domain-like	8085731	3002291	SCOP2 (2022-06-29)
M [auth L]	SCOP2 Family	Nqo4-like	8085742	4000433	SCOP2 (2022-06-29)
M [auth L]	SCOP2 Superfamily	HydB/Nqo4-like	8085743	3001849	SCOP2 (2022-06-29)
A [auth H]	SCOP2 Family	ND4 antiporter-like subunits	8059301	4005749	SCOP2 (2022-06-29)
A [auth H]	SCOP2 Superfamily	Antiporter subunits half-channel-like	8093345	3002280	SCOP2 (2022-06-29)
A [auth H]	SCOP2 Superfamily	Antiporter subunits half-channel-like	8059302	3002280	SCOP2 (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
B [auth G]	Oxidored_q2	e6cfwG1	A: alpha complex topology	X: NADH-quinone oxidoreductase subunit K (From Topology)	H: NADH-quinone oxidoreductase subunit K (From Topology)	T: NADH-quinone oxidoreductase subunit K	F: Oxidored_q2	ECOD (1.6)
E [auth M]	NADHdh	e6cfwM1	A: alpha complex topology	X: Sodium/proton antiporter subunits-like (From Homology)	H: Sodium/proton antiporter subunits-like	T: NADH-quinone oxidoreductase subunit 8 (Nqo8)-related	F: NADHdh	ECOD (1.6)
K [auth J]	Oxidored_q6	e6cfwJ1	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: CheY-like	F: Oxidored_q6	ECOD (1.6)
L [auth K]	Complex1_30kDa	e6cfwK1	A: a+b two layers	X: Nqo5-like	H: Nqo5-like (From Topology)	T: Nqo5-like	F: Complex1_30kDa	ECOD (1.6)
M [auth L]	Complex1_49kDa_1st	e6cfwL1	A: alpha complex topology	X: alpha-helical domain in nickel-iron hydrogenase, large subunit (From Topology)	H: alpha-helical domain in nickel-iron hydrogenase, large subunit (From Topology)	T: alpha-helical domain in nickel-iron hydrogenase, large subunit	F: Complex1_49kDa_1st	ECOD (1.6)
M [auth L]	NuoD	e6cfwL2	A: a+b two layers	X: FAD-linked reductases, C-terminal domain-like	H: Ni-Fe binding domain in nickel-iron hydrogenase large subunit (From Topology)	T: Ni-Fe binding domain in nickel-iron hydrogenase large subunit	F: NuoD	ECOD (1.6)
M [auth L]	NiFeSe_Hases_3rd_1	e6cfwL3	A: a+b two layers	X: FAD-linked reductases, C-terminal domain-like	H: Ni-Fe binding domain in nickel-iron hydrogenase large subunit (From Topology)	T: Ni-Fe binding domain in nickel-iron hydrogenase large subunit	F: NiFeSe_Hases_3rd_1	ECOD (1.6)
N	Fer4_21_1	e6cfwN1	A: a+b two layers	X: 4Fe-4S ferredoxin (From Topology)	H: 4Fe-4S ferredoxin (From Topology)	T: 4Fe-4S ferredoxin	F: Fer4_21_1	ECOD (1.6)
A [auth H]	Proton_antipo_M	e6cfwH1	A: alpha complex topology	X: Sodium/proton antiporter subunits-like (From Homology)	H: Sodium/proton antiporter subunits-like	T: NADH-quinone oxidoreductase subunit L (NuoL)-related	F: Proton_antipo_M	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
K [auth J]	3.40.50.12280	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C [auth D]	PF13244	MBH, subunit D (MbhD)	MBH, subunit D	Hydrogen gas-evolving membrane-bound hydrogenase (MBH) is a respiratory complex homologous to the quinone-reducing Complex I. Like Complex I, MBH has peripheral and membrane arms. MBH is made of 14 subunits (MbhA-N). MbhJ, K, L, N and M form the Memb ...	Hydrogen gas-evolving membrane-bound hydrogenase (MBH) is a respiratory complex homologous to the quinone-reducing Complex I. Like Complex I, MBH has peripheral and membrane arms. MBH is made of 14 subunits (MbhA-N). MbhJ, K, L, N and M form the Membrane-anchored hydrogenase module. MbhJ, K, L, N are predicted to be exposed to the cytoplasm and form the peripheral arm. The remaining 10 subunits are predicted to be integral membrane proteins forming the membrane arm, made of 44 transmembrane helices (TMH) [2, 3]. MbhA, B, C and F form the Sodium translocation module. MbhD, E, G and H form the Proton translocation module. MbhI is the linker between the hydrogenase module and the proton-translocating membrane module. It anchors the discontinuous TMH7 of MbhH via its middle lateral helix and the C-terminal of TMH2, found in MbhE. MbhD and MbhE together are equivalent to Nqo10 of Complex I [1]. MbhD has three TM helices.	Domain
K [auth J]	PF01058	NADH ubiquinone oxidoreductase, 20 Kd subunit (Oxidored_q6)	NADH ubiquinone oxidoreductase, 20 Kd subunit		Domain
L [auth K]	PF00329	Respiratory-chain NADH dehydrogenase, 30 Kd subunit (Complex1_30kDa)	Respiratory-chain NADH dehydrogenase, 30 Kd subunit		Domain
M [auth L]	PF00374	Nickel-dependent hydrogenase (NiFeSe_Hases)	Nickel-dependent hydrogenase	-	Family
M [auth L]	PF00346	Respiratory-chain NADH dehydrogenase, 49 Kd subunit (Complex1_49kDa)	Respiratory-chain NADH dehydrogenase, 49 Kd subunit	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B [auth G]	Monovalent cation/H+ antiporter subunit C	-	-	cell periphery cellular anatomical structure plasma membrane membrane
C [auth D]	MBH subunit	-	-	cell periphery cellular anatomical structure plasma membrane membrane
D [auth I]	MBH subunit	-	-	cellular anatomical structure membrane
E [auth M]	Mbh13 NADH dehydrogenase subunit	-	-	cell periphery cellular anatomical structure plasma membrane membrane
F	Monovalent cation/H+ antiporter subunit B	-	-	cell periphery cellular anatomical structure plasma membrane membrane
G [auth A]	Monovalent cation/H+ antiporter subunit E	monoatomic cation transmembrane transporter activity monoatomic ion transmembrane transporter activity transporter activity transmembrane transporter activity	-	cell periphery cellular anatomical structure plasma membrane membrane
I [auth C]	Monovalent cation/H+ antiporter subunit G	monoatomic cation transmembrane transporter activity metal cation:monoatomic cation antiporter activity proton transmembrane transporter activity sodium:proton antiporter activity sodium ion transmembrane transporter activity secondary active transmembrane transporter activity antiporter activity metal cation:proton antiporter activity active transmembrane transporter activity monoatomic ion transmembrane transporter activity transporter activity metal ion transmembrane transporter activity transmembrane transporter activity	-	cellular anatomical structure membrane
J [auth B]	Monovalent cation/H+ antiporter subunit F	monoatomic cation transmembrane transporter activity metal cation:monoatomic cation antiporter activity proton transmembrane transporter activity sodium:proton antiporter activity sodium ion transmembrane transporter activity secondary active transmembrane transporter activity antiporter activity metal cation:proton antiporter activity active transmembrane transporter activity monoatomic ion transmembrane transporter activity transporter activity metal ion transmembrane transporter activity transmembrane transporter activity	-	cell periphery cellular anatomical structure plasma membrane membrane
K [auth J]	Probable membrane-bound hydrogenase subunit mbhJ	oxidoreductase activity oxidoreductase activity, acting on hydrogen as donor, iron-sulfur protein as acceptor oxidoreductase activity, acting on hydrogen as donor ferredoxin hydrogenase activity catalytic activity iron-sulfur cluster binding binding 4 iron, 4 sulfur cluster binding metal cluster binding small molecule binding cation binding ion binding metal ion binding	ribose phosphate metabolic process ATP metabolic process ATP biosynthetic process nucleotide biosynthetic process carbohydrate derivative metabolic process purine ribonucleotide biosynthetic process purine ribonucleoside triphosphate biosynthetic process proton motive force-driven ATP synthesis nucleobase-containing compound metabolic process ribonucleotide biosynthetic process purine nucleotide metabolic process ribonucleotide metabolic process purine nucleoside triphosphate biosynthetic process nucleobase-containing small molecule metabolic process purine-containing compound biosynthetic process ribose phosphate metabolic process ATP metabolic process ATP biosynthetic process nucleotide biosynthetic process carbohydrate derivative metabolic process purine ribonucleotide biosynthetic process purine ribonucleoside triphosphate biosynthetic process proton motive force-driven ATP synthesis nucleobase-containing compound metabolic process ribonucleotide biosynthetic process purine nucleotide metabolic process ribonucleotide metabolic process purine nucleoside triphosphate biosynthetic process nucleobase-containing small molecule metabolic process purine-containing compound biosynthetic process purine ribonucleoside triphosphate metabolic process phosphate-containing compound metabolic process small molecule metabolic process phosphorus metabolic process ribose phosphate biosynthetic process nucleoside phosphate metabolic process carbohydrate derivative biosynthetic process purine nucleoside triphosphate metabolic process nucleoside triphosphate biosynthetic process primary metabolic process nucleotide metabolic process nucleobase-containing compound biosynthetic process ribonucleoside triphosphate biosynthetic process purine-containing compound metabolic process biosynthetic process organophosphate metabolic process organophosphate biosynthetic process nucleoside phosphate biosynthetic process metabolic process cellular process nucleoside triphosphate metabolic process purine ribonucleotide metabolic process purine nucleotide biosynthetic process	cell periphery cellular anatomical structure plasma membrane membrane protein-containing complex catalytic complex oxidoreductase complex ferredoxin hydrogenase complex intracellular protein-containing complex
L [auth K]	Membrane-bound hydrogenase subunit beta	oxidoreductase activity oxidoreductase activity, acting on hydrogen as donor, iron-sulfur protein as acceptor oxidoreductase activity, acting on hydrogen as donor ferredoxin hydrogenase activity catalytic activity cation binding ion binding binding metal ion binding small molecule binding monoatomic cation transmembrane transporter activity proton transmembrane transporter activity primary active transmembrane transporter activity electron transfer activity oxidoreductase activity oxidoreductase activity, acting on hydrogen as donor, iron-sulfur protein as acceptor oxidoreductase activity, acting on hydrogen as donor ferredoxin hydrogenase activity catalytic activity cation binding ion binding binding metal ion binding small molecule binding monoatomic cation transmembrane transporter activity proton transmembrane transporter activity primary active transmembrane transporter activity electron transfer activity active monoatomic ion transmembrane transporter activity NADH dehydrogenase (ubiquinone) activity oxidoreduction-driven active transmembrane transporter activity active transmembrane transporter activity monoatomic ion transmembrane transporter activity transporter activity transmembrane transporter activity	ribose phosphate metabolic process ATP metabolic process ATP biosynthetic process nucleotide biosynthetic process carbohydrate derivative metabolic process purine ribonucleotide biosynthetic process purine ribonucleoside triphosphate biosynthetic process proton motive force-driven ATP synthesis nucleobase-containing compound metabolic process ribonucleotide biosynthetic process purine nucleotide metabolic process ribonucleotide metabolic process purine nucleoside triphosphate biosynthetic process nucleobase-containing small molecule metabolic process purine-containing compound biosynthetic process ribose phosphate metabolic process ATP metabolic process ATP biosynthetic process nucleotide biosynthetic process carbohydrate derivative metabolic process purine ribonucleotide biosynthetic process purine ribonucleoside triphosphate biosynthetic process proton motive force-driven ATP synthesis nucleobase-containing compound metabolic process ribonucleotide biosynthetic process purine nucleotide metabolic process ribonucleotide metabolic process purine nucleoside triphosphate biosynthetic process nucleobase-containing small molecule metabolic process purine-containing compound biosynthetic process purine ribonucleoside triphosphate metabolic process phosphate-containing compound metabolic process small molecule metabolic process phosphorus metabolic process ribose phosphate biosynthetic process nucleoside phosphate metabolic process carbohydrate derivative biosynthetic process purine nucleoside triphosphate metabolic process nucleoside triphosphate biosynthetic process primary metabolic process nucleotide metabolic process nucleobase-containing compound biosynthetic process ribonucleoside triphosphate biosynthetic process purine-containing compound metabolic process biosynthetic process organophosphate metabolic process organophosphate biosynthetic process nucleoside phosphate biosynthetic process metabolic process cellular process nucleoside triphosphate metabolic process purine ribonucleotide metabolic process purine nucleotide biosynthetic process	cell periphery cellular anatomical structure plasma membrane membrane protein-containing complex catalytic complex oxidoreductase complex ferredoxin hydrogenase complex intracellular protein-containing complex
M [auth L]	Membrane-bound hydrogenase subunit alpha	cation binding transition metal ion binding ion binding binding nickel cation binding metal ion binding small molecule binding oxidoreductase activity oxidoreductase activity, acting on hydrogen as donor, iron-sulfur protein as acceptor oxidoreductase activity, acting on hydrogen as donor ferredoxin hydrogenase activity catalytic activity NAD binding nucleoside phosphate binding cation binding transition metal ion binding ion binding binding nickel cation binding metal ion binding small molecule binding oxidoreductase activity oxidoreductase activity, acting on hydrogen as donor, iron-sulfur protein as acceptor oxidoreductase activity, acting on hydrogen as donor ferredoxin hydrogenase activity catalytic activity NAD binding nucleoside phosphate binding purine nucleotide binding adenyl nucleotide binding nucleotide binding heterocyclic compound binding oxidoreductase activity, acting on NAD(P)H quinone binding	ribose phosphate metabolic process ATP metabolic process ATP biosynthetic process nucleotide biosynthetic process carbohydrate derivative metabolic process purine ribonucleotide biosynthetic process purine ribonucleoside triphosphate biosynthetic process proton motive force-driven ATP synthesis nucleobase-containing compound metabolic process ribonucleotide biosynthetic process purine nucleotide metabolic process ribonucleotide metabolic process purine nucleoside triphosphate biosynthetic process nucleobase-containing small molecule metabolic process purine-containing compound biosynthetic process ribose phosphate metabolic process ATP metabolic process ATP biosynthetic process nucleotide biosynthetic process carbohydrate derivative metabolic process purine ribonucleotide biosynthetic process purine ribonucleoside triphosphate biosynthetic process proton motive force-driven ATP synthesis nucleobase-containing compound metabolic process ribonucleotide biosynthetic process purine nucleotide metabolic process ribonucleotide metabolic process purine nucleoside triphosphate biosynthetic process nucleobase-containing small molecule metabolic process purine-containing compound biosynthetic process purine ribonucleoside triphosphate metabolic process phosphate-containing compound metabolic process small molecule metabolic process phosphorus metabolic process ribose phosphate biosynthetic process nucleoside phosphate metabolic process carbohydrate derivative biosynthetic process purine nucleoside triphosphate metabolic process nucleoside triphosphate biosynthetic process primary metabolic process nucleotide metabolic process nucleobase-containing compound biosynthetic process ribonucleoside triphosphate biosynthetic process purine-containing compound metabolic process biosynthetic process organophosphate metabolic process organophosphate biosynthetic process nucleoside phosphate biosynthetic process metabolic process cellular process nucleoside triphosphate metabolic process purine ribonucleotide metabolic process purine nucleotide biosynthetic process	cell periphery cellular anatomical structure plasma membrane membrane protein-containing complex catalytic complex oxidoreductase complex ferredoxin hydrogenase complex intracellular protein-containing complex
N	NADH-plastoquinone oxidoreductase subunit	oxidoreductase activity oxidoreductase activity, acting on NAD(P)H catalytic activity iron-sulfur cluster binding binding 4 iron, 4 sulfur cluster binding metal cluster binding small molecule binding quinone binding	-	cellular anatomical structure membrane
H [auth E]	MBH subunit	-	-	cellular anatomical structure membrane
A [auth H]	Monovalent cation/H+ antiporter subunit D	-	-	cell periphery cellular anatomical structure plasma membrane membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B [auth G]	IPR039428	NADH-ubiquinone oxidoreductase chain 4L/Mnh complex subunit C1-like	Family
B [auth G]	IPR050601	CPA3 antiporter subunit C	Family
C [auth D]	IPR025383	MrpA C-terminal/MbhD	Domain
C [auth D]	IPR042106	NADH-ubiquinone/plastoquinone oxidoreductase chain 6, subunit NuoJ	Homologous Superfamily
E [auth M]	IPR001694	NADH:ubiquinone oxidoreductase, subunit 1/F420H2 oxidoreductase subunit H	Family
E [auth M]	IPR052561	Complex I Subunit 1	Family
F	IPR050622	CPA3 Na(+)/H(+) Antiporter Subunit B	Family
F	IPR007182	Na+/H+ antiporter MnhB subunit-related protein	Domain
G [auth A]	IPR002758	Na+/H+ antiporter subunit E	Family
I [auth C]	IPR005133	Na+/H+ antiporter subunit G	Family
J [auth B]	IPR007208	Na(+)/H(+) antiporter subunit F-like	Family
K [auth J]	IPR052375	Complex I 20 kDa subunit-like	Family
K [auth J]	IPR006137	NADH:ubiquinone oxidoreductase-like, 20kDa subunit	Domain
L [auth K]	IPR037232	NADH:ubiquinone oxidoreductase, 30kDa subunit superfamily	Homologous Superfamily
L [auth K]	IPR001268	NADH:ubiquinone oxidoreductase, 30kDa subunit	Domain
M [auth L]	IPR052197	Complex I 49 kDa subunit-like	Family
M [auth L]	IPR001501	Nickel-dependent hydrogenase, large subunit	Family
M [auth L]	IPR029014	[NiFe]-hydrogenase, large subunit	Homologous Superfamily
M [auth L]	IPR001135	NADH-quinone oxidoreductase, subunit D	Domain
N	IPR017900	4Fe-4S ferredoxin, iron-sulphur binding, conserved site	Conserved Site
N	IPR017896	4Fe-4S ferredoxin-type, iron-sulphur binding domain	Domain
N	IPR010226	NADH-quinone oxidoreductase, chain I	Family
H [auth E]	IPR046806	MrpA C-terminal/MbhE	Domain
A [auth H]	IPR050586	CPA3 Na+/H+ Antiporter Subunit D	Family
A [auth H]	IPR001516	NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminal	Domain
A [auth H]	IPR001750	NADH:quinone oxidoreductase/Mrp antiporter, transmembrane domain	Domain

Membrane Protein Annotation: OPM OPM Database Homepage

Chains	External Link	Type	Class	Superfamily	Family
A [auth H], B [auth G], C [auth D], D [auth I], E [auth M] A [auth H], B [auth G], C [auth D], D [auth I], E [auth M], F, G [auth A], H [auth E], I [auth C], J [auth B], K [auth J], L [auth K], M [auth L], N	OPM	Transmembrane	Alpha-helical polytopic	Electron transport chain complex I (NADH dehydrogenase) and supercomplexes	H+ or Na+ translocating NADH dehydrogenase

Membrane Protein Annotation: PDBTM PDBTM Database Homepage

Chains	External Link	Comment
A [auth H], B [auth G], C [auth D], D [auth I], E [auth M] A [auth H], B [auth G], C [auth D], D [auth I], E [auth M], F, G [auth A], H [auth E], I [auth C], J [auth B], K [auth J], L [auth K], M [auth L], N	PDBTM	Annotated as membrane protein by PDBTM

Membrane Protein Annotation: MemProtMD MemProtMD Database Homepage

Chains	External Link	Comment
A [auth H], B [auth G], C [auth D], D [auth I], E [auth M] A [auth H], B [auth G], C [auth D], D [auth I], E [auth M], F, G [auth A], H [auth E], I [auth C], J [auth B], K [auth J], L [auth K], M [auth L], N	MemProtMD	Annotated as membrane protein by MemProtMD

Membrane Protein Annotation: mpstruc mpstruc Database Homepage

Chains	Resource Link	Group	Subgroup	Protein
A [auth H], B [auth G], C [auth D], D [auth I], E [auth M] A [auth H], B [auth G], C [auth D], D [auth I], E [auth M], F, G [auth A], H [auth E], I [auth C], J [auth B], K [auth J], L [auth K], M [auth L], N	mpstruc	TRANSMEMBRANE PROTEINS: ALPHA-HELICAL	Electron Transport Chain Complexes: Complex I	Membrane-bound hydrogenase ancient respiratory system