6U8Y | pdb_00006u8y

Structure of the membrane-bound sulfane sulfur reductase (MBS), an archaeal respiratory membrane complex

External Resource: Annotation

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

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
V [auth j]	SCOP2 Family	Nq06/HydA N-terminal domain-like	8097965	4007641	SCOP2 (2022-06-29)
V [auth j]	SCOP2 Superfamily	Nqo6/HydA N-terminal domain-like	8097966	3002291	SCOP2 (2022-06-29)
I [auth J]	SCOP2B Superfamily	Nqo6/HydA N-terminal domain-like	8097966	3002291	SCOP2B (2022-06-29)
S [auth g]	SCOP2 Family	NADH-quinone oxidoreductase NDH subunit 11-like	8097963	4005793	SCOP2 (2022-06-29)
S [auth g]	SCOP2 Superfamily	NADH-quinone oxidoreductase, subunit 11-like	8097964	3002200	SCOP2 (2022-06-29)
F [auth G]	SCOP2B Superfamily	NADH-quinone oxidoreductase, subunit 11-like	8097964	3002200	SCOP2B (2022-06-29)
P [auth c]	SCOP2 Family	Monovalent cation/H+ antiporter MBH, subunit G	8097961	4007805	SCOP2 (2022-06-29)
P [auth c]	SCOP2 Superfamily	NADH-quinone oxidoreductase, subunit 11-like	8097962	3002200	SCOP2 (2022-06-29)
C	SCOP2B Superfamily	NADH-quinone oxidoreductase, subunit 11-like	8097962	3002200	SCOP2B (2022-06-29)
O [auth b]	SCOP2 Family	Monovalent cation/H+ antiporter MBH, subunit F	8097967	4007804	SCOP2 (2022-06-29)
O [auth b]	SCOP2 Superfamily	NADH-quinone oxidoreductase, subunit 11-like	8097968	3002200	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	NADH-quinone oxidoreductase, subunit 11-like	8097968	3002200	SCOP2B (2022-06-29)
X [auth l]	SCOP2 Family	Nqo4-like	8097969	4000433	SCOP2 (2022-06-29)
X [auth l]	SCOP2 Superfamily	HydB/Nqo4-like	8097970	3001849	SCOP2 (2022-06-29)
K [auth L]	SCOP2B Superfamily	HydB/Nqo4-like	8097970	3001849	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
V [auth j]	Oxidored_q6	e6u8yj1	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: CheY-like	F: Oxidored_q6	ECOD (1.6)
I [auth J]	Oxidored_q6	e6u8yJ1	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: CheY-like	F: Oxidored_q6	ECOD (1.6)
U [auth x]	Proton_antipo_M	e6u8yx1	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)
H [auth X]	Proton_antipo_M	e6u8yX1	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)
T [auth h]	Proton_antipo_M	e6u8yh1	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)
G [auth H]	Proton_antipo_M	e6u8yH1	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)
S [auth g]	Oxidored_q2	e6u8yg1	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)
F [auth G]	Oxidored_q2	e6u8yG1	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)
Y [auth m]	NADHdh	e6u8ym1	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)
L [auth M]	NADHdh	e6u8yM1	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)
X [auth l]	Complex1_49kDa_1st	e6u8yl3	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)
X [auth l]	NuoD	e6u8yl2	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)
X [auth l]	Complex1_49kDa_2nd	e6u8yl1	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: Complex1_49kDa_2nd	ECOD (1.6)
K [auth L]	Complex1_49kDa_1st	e6u8yL1	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)
K [auth L]	NuoD	e6u8yL2	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)
K [auth L]	Complex1_49kDa_2nd	e6u8yL3	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: Complex1_49kDa_2nd	ECOD (1.6)
W [auth k]	Complex1_30kDa	e6u8yk1	A: a+b two layers	X: Nqo5-like	H: Nqo5-like (From Topology)	T: Nqo5-like	F: Complex1_30kDa	ECOD (1.6)
J [auth K]	Complex1_30kDa	e6u8yK1	A: a+b two layers	X: Nqo5-like	H: Nqo5-like (From Topology)	T: Nqo5-like	F: Complex1_30kDa	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
I [auth J], V [auth j]	PF01058	NADH ubiquinone oxidoreductase, 20 Kd subunit (Oxidored_q6)	NADH ubiquinone oxidoreductase, 20 Kd subunit		Domain
H [auth X], U [auth x]	PF00361	NADH:quinone oxidoreductase/Mrp antiporter, TM (Proton_antipo_M)	NADH:quinone oxidoreductase/Mrp antiporter, TM	This entry includes membrane transporters and represents some 7 of potentially 14-16 TM regions. In many instances, its members forms part of complex I that catalyses the transfer of two electrons from NADH to ubiquinone in a reaction that is associa ...	This entry includes membrane transporters and represents some 7 of potentially 14-16 TM regions. In many instances, its members forms part of complex I that catalyses the transfer of two electrons from NADH to ubiquinone in a reaction that is associated with proton translocation across the membrane, and in this context is a combination predominantly of subunits 2, 4, 5, 14, L, M and N [1]. In many bacterial species these proteins are probable stand-alone transporters not coupled with oxidoreduction [2].	Domain
G [auth H], T [auth h]	PF00361	NADH:quinone oxidoreductase/Mrp antiporter, TM (Proton_antipo_M)	NADH:quinone oxidoreductase/Mrp antiporter, TM	This entry includes membrane transporters and represents some 7 of potentially 14-16 TM regions. In many instances, its members forms part of complex I that catalyses the transfer of two electrons from NADH to ubiquinone in a reaction that is associa ...	This entry includes membrane transporters and represents some 7 of potentially 14-16 TM regions. In many instances, its members forms part of complex I that catalyses the transfer of two electrons from NADH to ubiquinone in a reaction that is associated with proton translocation across the membrane, and in this context is a combination predominantly of subunits 2, 4, 5, 14, L, M and N [1]. In many bacterial species these proteins are probable stand-alone transporters not coupled with oxidoreduction [2].	Domain
F [auth G], S [auth g]	PF00420	NADH-ubiquinone/plastoquinone oxidoreductase chain 4L (Oxidored_q2)	NADH-ubiquinone/plastoquinone oxidoreductase chain 4L	-	Family
E, R [auth e]	PF04039	Domain related to MnhB subunit of Na+/H+ antiporter (MnhB)	Domain related to MnhB subunit of Na+/H+ antiporter	-	Family
E, R [auth e]	PF20501	MBH, subunit E (MbhE)	MBH, subunit E	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]. MbhE has two transmembrane helices: TMH1 and TMH2.	Domain
D, Q [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
C, P [auth c]	PF03334	Na+/H+ antiporter subunit (PhaG_MnhG_YufB)	Na+/H+ antiporter subunit	-	Family
B, O [auth b]	PF04066	Multiple resistance and pH regulation protein F (MrpF / PhaF) (MrpF_PhaF)	Multiple resistance and pH regulation protein F (MrpF / PhaF)	-	Family
M [auth N], Z [auth n]	PF12838	4Fe-4S dicluster domain (Fer4_7)	4Fe-4S dicluster domain	Superfamily includes proteins containing domains which bind to iron-sulfur clusters. Members include bacterial ferredoxins, various dehydrogenases, and various reductases. Structure of the domain is an alpha-antiparallel beta sandwich. Domain contai ...	Superfamily includes proteins containing domains which bind to iron-sulfur clusters. Members include bacterial ferredoxins, various dehydrogenases, and various reductases. Structure of the domain is an alpha-antiparallel beta sandwich. Domain contains two 4Fe4S clusters.	Domain
L [auth M], Y [auth m]	PF00146	NADH dehydrogenase (NADHdh)	NADH dehydrogenase	-	Family
K [auth L], X [auth l]	PF00346	Respiratory-chain NADH dehydrogenase, 49 Kd subunit (Complex1_49kDa)	Respiratory-chain NADH dehydrogenase, 49 Kd subunit	-	Family
J [auth K], W [auth k]	PF00329	Respiratory-chain NADH dehydrogenase, 30 Kd subunit (Complex1_30kDa)	Respiratory-chain NADH dehydrogenase, 30 Kd subunit		Domain
A, N [auth a]	PF01899	Na+/H+ ion antiporter subunit (MNHE)	Na+/H+ ion antiporter subunit	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
I [auth J], V [auth j]	NADH dehydrogenase subunit B	iron-sulfur cluster binding binding 4 iron, 4 sulfur cluster binding metal cluster binding small molecule binding cation binding ion binding metal ion 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 iron-sulfur cluster binding binding 4 iron, 4 sulfur cluster binding metal cluster binding small molecule binding cation binding ion binding metal ion 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 quinone binding	electron transport coupled proton transport transport proton transmembrane transport monoatomic ion transmembrane transport establishment of localization monoatomic cation transmembrane transport transmembrane transport localization energy coupled proton transmembrane transport, against electrochemical gradient monoatomic ion transport cellular process monoatomic cation transport aerobic respiration cellular respiration electron transport coupled proton transport transport proton transmembrane transport monoatomic ion transmembrane transport establishment of localization monoatomic cation transmembrane transport transmembrane transport localization energy coupled proton transmembrane transport, against electrochemical gradient monoatomic ion transport cellular process monoatomic cation transport aerobic respiration cellular respiration energy derivation by oxidation of organic compounds metabolic process generation of precursor metabolites and energy	respiratory chain complex protein-containing complex catalytic complex membrane membrane protein complex transporter complex NADH dehydrogenase complex cellular anatomical structure transmembrane transporter complex respiratory chain complex I oxidoreductase complex
H [auth X], U [auth x]	NADH dehydrogenase subunit M	-	-	cell periphery cellular anatomical structure plasma membrane membrane
G [auth H], T [auth h]	NADH dehydrogenase subunit N	-	-	cell periphery cellular anatomical structure plasma membrane membrane
F [auth G], S [auth g]	Monovalent cation/H+ antiporter subunit C	-	-	cell periphery cellular anatomical structure plasma membrane membrane
E, R [auth e]	Monovalent cation/H+ antiporter subunit B	-	-	cell periphery cellular anatomical structure plasma membrane membrane
D, Q [auth d]	DUF4040 domain-containing protein	-	-	cell periphery cellular anatomical structure plasma membrane membrane
C, P [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
B, O [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
M [auth N], Z [auth n]	NADH dehydrogenase subunit I	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
L [auth M], Y [auth m]	NADH dehydrogenase subunit	-	-	cell periphery cellular anatomical structure plasma membrane membrane
K [auth L], X [auth l]	NADH dehydrogenase subunit D	NAD binding binding nucleoside phosphate binding purine nucleotide binding adenyl nucleotide binding nucleotide binding heterocyclic compound binding small molecule binding oxidoreductase activity oxidoreductase activity, acting on NAD(P)H catalytic activity quinone binding	-	-
J [auth K], W [auth k]	NADH dehydrogenase subunit C	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	-	-
A, N [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

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
I [auth J], V [auth j]	IPR006138	NADH-ubiquinone oxidoreductase, 20 Kd subunit	Family
I [auth J], V [auth j]	IPR006137	NADH:ubiquinone oxidoreductase-like, 20kDa subunit	Domain
H [auth X], U [auth x]	IPR050586	CPA3 Na+/H+ Antiporter Subunit D	Family
H [auth X], U [auth x]	IPR001750	NADH:quinone oxidoreductase/Mrp antiporter, transmembrane domain	Domain
G [auth H], T [auth h]	IPR050586	CPA3 Na+/H+ Antiporter Subunit D	Family
G [auth H], T [auth h]	IPR001750	NADH:quinone oxidoreductase/Mrp antiporter, transmembrane domain	Domain
F [auth G], S [auth g]	IPR039428	NADH-ubiquinone oxidoreductase chain 4L/Mnh complex subunit C1-like	Family
F [auth G], S [auth g]	IPR050601	CPA3 antiporter subunit C	Family
E, R [auth e]	IPR050622	CPA3 Na(+)/H(+) Antiporter Subunit B	Family
E, R [auth e]	IPR007182	Na+/H+ antiporter MnhB subunit-related protein	Domain
E, R [auth e]	IPR046806	MrpA C-terminal/MbhE	Domain
D, Q [auth d]	IPR025383	MrpA C-terminal/MbhD	Domain
D, Q [auth d]	IPR042106	NADH-ubiquinone/plastoquinone oxidoreductase chain 6, subunit NuoJ	Homologous Superfamily
C, P [auth c]	IPR005133	Na+/H+ antiporter subunit G	Family
B, O [auth b]	IPR007208	Na(+)/H(+) antiporter subunit F-like	Family
M [auth N], Z [auth n]	IPR017900	4Fe-4S ferredoxin, iron-sulphur binding, conserved site	Conserved Site
M [auth N], Z [auth n]	IPR017896	4Fe-4S ferredoxin-type, iron-sulphur binding domain	Domain
M [auth N], Z [auth n]	IPR010226	NADH-quinone oxidoreductase, chain I	Family
L [auth M], Y [auth m]	IPR001694	NADH:ubiquinone oxidoreductase, subunit 1/F420H2 oxidoreductase subunit H	Family
L [auth M], Y [auth m]	IPR052561	Complex I Subunit 1	Family
K [auth L], X [auth l]	IPR022885	NAD(P)H-quinone oxidoreductase subunit D/H	Family
K [auth L], X [auth l]	IPR014029	NADH:ubiquinone oxidoreductase, 49kDa subunit, conserved site	Conserved Site
K [auth L], X [auth l]	IPR029014	[NiFe]-hydrogenase, large subunit	Homologous Superfamily
K [auth L], X [auth l]	IPR001135	NADH-quinone oxidoreductase, subunit D	Domain
J [auth K], W [auth k]	IPR037232	NADH:ubiquinone oxidoreductase, 30kDa subunit superfamily	Homologous Superfamily
J [auth K], W [auth k]	IPR001268	NADH:ubiquinone oxidoreductase, 30kDa subunit	Domain
A, N [auth a]	IPR002758	Na+/H+ antiporter subunit E	Family

Membrane Protein Annotation: OPM OPM Database Homepage

Chains	External Link	Type	Class	Superfamily	Family
A, B, C, D, E A, B, C, D, E, F [auth G], G [auth H], H [auth X], L [auth M], M [auth N], N [auth a], O [auth b], P [auth c], Q [auth d], R [auth e], S [auth g], T [auth h], U [auth x], Y [auth m], Z [auth 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, B, C, D, E A, B, C, D, E, F [auth G], G [auth H], H [auth X], L [auth M], M [auth N], N [auth a], O [auth b], P [auth c], Q [auth d], R [auth e], S [auth g], T [auth h], U [auth x], Y [auth m], Z [auth n]	PDBTM	Annotated as membrane protein by PDBTM