8BEE

Cryo-EM structure of the Arabidopsis thaliana I+III2 supercomplex (CI peripheral core)

External Resource: Annotation

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

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A [auth B]	SCOP2B Superfamily	Nqo6/HydA N-terminal domain-like	8101623	3002291	SCOP2B (2022-06-29)
C [auth D]	SCOP2B Superfamily	HydB/Nqo4-like	8101589	3001849	SCOP2B (2022-06-29)
F [auth U]	SCOP2B Superfamily	ACP-like	8101483	3001805	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)
A [auth B]	Oxidored_q6	e8beeB1	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: CheY-like	F: Oxidored_q6	ECOD (1.6)
B [auth C]	Complex1_30kDa	e8beeC1	A: a+b two layers	X: Nqo5-like	H: Nqo5-like (From Topology)	T: Nqo5-like	F: Complex1_30kDa	ECOD (1.6)
C [auth D]	Complex1_49kDa_1st	e8beeD2	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)
C [auth D]	NuoD	e8beeD1	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)
C [auth D]	Complex1_49kDa_2nd	e8beeD3	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)
D [auth I]	Fer4_21_1	e8beeI1	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)
E [auth P]	NmrA	e8beeP1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NAD(P)-binding Rossmann-fold domains	F: NmrA	ECOD (1.6)
F [auth U]	PP-binding	e8beeU1	A: alpha bundles	X: ACP-like	H: Acyl-carrier protein (ACP) (From Topology)	T: Acyl-carrier protein (ACP)	F: PP-binding	ECOD (1.6)
H [auth W]	Complex1_LYR	e8beeW1	A: alpha bundles	X: LYR protein (From Topology)	H: LYR protein (From Topology)	T: LYR protein	F: Complex1_LYR	ECOD (1.6)
J [auth q]	NDUFA12	e8beeq1	A: a+b three layers	X: Mitochondrial complex I, B17.2 subunit (From Topology)	H: Mitochondrial complex I, B17.2 subunit (From Topology)	T: Mitochondrial complex I, B17.2 subunit	F: NDUFA12	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A [auth B]	PF01058	NADH ubiquinone oxidoreductase, 20 Kd subunit (Oxidored_q6)	NADH ubiquinone oxidoreductase, 20 Kd subunit	-	Family
B [auth C]	PF00329	Respiratory-chain NADH dehydrogenase, 30 Kd subunit (Complex1_30kDa)	Respiratory-chain NADH dehydrogenase, 30 Kd subunit	-	Family
C [auth D]	PF00346	Respiratory-chain NADH dehydrogenase, 49 Kd subunit (Complex1_49kDa)	Respiratory-chain NADH dehydrogenase, 49 Kd subunit	-	Family
D [auth I]	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
E [auth P]	PF01370	NAD dependent epimerase/dehydratase family (Epimerase)	NAD dependent epimerase/dehydratase family	-	Family
F [auth U]	PF00550	Phosphopantetheine attachment site (PP-binding)	Phosphopantetheine attachment site	A 4'-phosphopantetheine prosthetic group is attached through a serine. This prosthetic group acts as a a 'swinging arm' for the attachment of activated fatty acid and amino-acid groups. This domain forms a four helix bundle. This family includes memb ...	A 4'-phosphopantetheine prosthetic group is attached through a serine. This prosthetic group acts as a a 'swinging arm' for the attachment of activated fatty acid and amino-acid groups. This domain forms a four helix bundle. This family includes members not included in Prosite. The inclusion of these members is supported by sequence analysis and functional evidence. The related domain of Swiss:P19828 has the attachment serine replaced by an alanine.	Domain
I [auth Z]	PF06212	GRIM-19 protein (GRIM-19)	GRIM-19 protein	-	Family
G [auth V]	PF04716	ETC complex I subunit conserved region (ETC_C1_NDUFA5)	ETC complex I subunit conserved region	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth B]	NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial	cation binding transition metal ion binding zinc ion binding ion binding binding metal ion binding small molecule binding iron-sulfur cluster binding 4 iron, 4 sulfur cluster binding metal cluster binding monoatomic cation transmembrane transporter activity proton transmembrane transporter activity primary active transmembrane transporter activity oxidoreductase activity, acting on NAD(P)H cation binding transition metal ion binding zinc ion binding ion binding binding metal ion binding small molecule binding iron-sulfur cluster binding 4 iron, 4 sulfur cluster binding metal cluster binding monoatomic cation transmembrane transporter activity proton transmembrane transporter activity primary active transmembrane transporter activity oxidoreductase activity, acting on NAD(P)H oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor electron transfer activity active monoatomic ion transmembrane transporter activity oxidoreductase activity NADH dehydrogenase (ubiquinone) activity oxidoreduction-driven active transmembrane transporter activity active transmembrane transporter activity inorganic molecular entity transmembrane transporter activity inorganic cation transmembrane transporter activity monoatomic ion transmembrane transporter activity transporter activity transmembrane transporter activity catalytic activity quinone binding	-	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle cell periphery plasma membrane membrane
B [auth C]	NADH dehydrogenase [ubiquinone] iron-sulfur protein 3	monoatomic cation transmembrane transporter activity proton transmembrane transporter activity primary active transmembrane transporter activity oxidoreductase activity, acting on NAD(P)H oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor electron transfer activity active monoatomic ion transmembrane transporter activity oxidoreductase activity NADH dehydrogenase (ubiquinone) activity oxidoreduction-driven active transmembrane transporter activity active transmembrane transporter activity inorganic molecular entity transmembrane transporter activity inorganic cation transmembrane transporter activity monoatomic ion transmembrane transporter activity transporter activity monoatomic cation transmembrane transporter activity proton transmembrane transporter activity primary active transmembrane transporter activity oxidoreductase activity, acting on NAD(P)H oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor electron transfer activity active monoatomic ion transmembrane transporter activity oxidoreductase activity NADH dehydrogenase (ubiquinone) activity oxidoreduction-driven active transmembrane transporter activity active transmembrane transporter activity inorganic molecular entity transmembrane transporter activity inorganic cation transmembrane transporter activity monoatomic ion transmembrane transporter activity transporter activity transmembrane transporter activity catalytic activity	-	membrane-bounded organelle mitochondrial membrane intracellular anatomical structure organelle inner membrane mitochondrion membrane intracellular membrane-bounded organelle mitochondrial inner membrane intracellular organelle organelle envelope cellular anatomical structure mitochondrial envelope organelle cytoplasm membrane-bounded organelle mitochondrial membrane intracellular anatomical structure organelle inner membrane mitochondrion membrane intracellular membrane-bounded organelle mitochondrial inner membrane intracellular organelle organelle envelope cellular anatomical structure mitochondrial envelope organelle cytoplasm organelle membrane respiratory chain complex protein-containing complex catalytic complex membrane protein complex transporter complex NADH dehydrogenase complex transmembrane transporter complex respiratory chain complex I oxidoreductase complex
C [auth D]	NADH dehydrogenase subunit 7	NAD binding binding nucleoside phosphate binding purine nucleotide binding organic cyclic compound binding adenyl nucleotide binding nucleotide binding heterocyclic compound binding small molecule binding monoatomic cation transmembrane transporter activity proton transmembrane transporter activity primary active transmembrane transporter activity oxidoreductase activity, acting on NAD(P)H oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor NAD binding binding nucleoside phosphate binding purine nucleotide binding organic cyclic compound binding adenyl nucleotide binding nucleotide binding heterocyclic compound binding small molecule binding monoatomic cation transmembrane transporter activity proton transmembrane transporter activity primary active transmembrane transporter activity oxidoreductase activity, acting on NAD(P)H oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor electron transfer activity active monoatomic ion transmembrane transporter activity oxidoreductase activity NADH dehydrogenase (ubiquinone) activity oxidoreduction-driven active transmembrane transporter activity active transmembrane transporter activity inorganic molecular entity transmembrane transporter activity inorganic cation transmembrane transporter activity monoatomic ion transmembrane transporter activity transporter activity transmembrane transporter activity catalytic activity quinone binding	aerobic respiration cellular respiration aerobic electron transport chain oxidative phosphorylation energy derivation by oxidation of organic compounds ATP synthesis coupled electron transport electron transport chain generation of precursor metabolites and energy mitochondrial electron transport, NADH to ubiquinone respiratory electron transport chain metabolic process cellular process mitochondrial ATP synthesis coupled electron transport	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle respiratory chain complex protein-containing complex catalytic complex membrane membrane protein complex transporter complex membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle respiratory chain complex protein-containing complex catalytic complex membrane membrane protein complex transporter complex NADH dehydrogenase complex transmembrane transporter complex respiratory chain complex I oxidoreductase complex
D [auth I]	NADH dehydrogenase [ubiquinone] iron-sulfur protein 8-A, mitochondrial	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 oxidoreductase activity, acting on NAD(P)H oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor electron transfer 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 oxidoreductase activity, acting on NAD(P)H oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor electron transfer activity active monoatomic ion transmembrane transporter activity oxidoreductase activity NADH dehydrogenase (ubiquinone) activity oxidoreduction-driven active transmembrane transporter activity active transmembrane transporter activity inorganic molecular entity transmembrane transporter activity inorganic cation transmembrane transporter activity monoatomic ion transmembrane transporter activity transporter activity transmembrane transporter activity catalytic activity	-	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle membrane
E [auth P]	NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mitochondrial	-	-	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle membrane-enclosed lumen mitochondrial matrix intracellular organelle lumen organelle lumen
F [auth U]	Acyl carrier protein 2, mitochondrial	cation binding transition metal ion binding ion binding binding metal ion binding cobalt ion binding small molecule binding phosphopantetheine-dependent carrier activity prosthetic group binding acyl carrier activity molecular carrier activity ACP phosphopantetheine attachment site binding	transport proton transmembrane transport monoatomic ion transmembrane transport inorganic ion transmembrane transport establishment of localization inorganic cation transmembrane transport transmembrane transport monoatomic cation transmembrane transport localization monoatomic ion transport cellular process monoatomic cation transport aerobic respiration cellular respiration transport proton transmembrane transport monoatomic ion transmembrane transport inorganic ion transmembrane transport establishment of localization inorganic cation transmembrane transport transmembrane transport monoatomic cation transmembrane transport localization monoatomic ion transport cellular process monoatomic cation transport aerobic respiration cellular respiration aerobic electron transport chain oxidative phosphorylation energy derivation by oxidation of organic compounds ATP synthesis coupled electron transport electron transport chain generation of precursor metabolites and energy mitochondrial electron transport, NADH to ubiquinone respiratory electron transport chain metabolic process mitochondrial ATP synthesis coupled electron transport	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle cytosol membrane-enclosed lumen mitochondrial matrix intracellular organelle lumen organelle lumen nucleus
H [auth W]	NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6	-	-	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle intracellular organelle mitochondrion organelle intracellular membrane-bounded organelle mitochondrial membrane organelle inner membrane membrane mitochondrial inner membrane organelle envelope cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle intracellular organelle mitochondrion organelle intracellular membrane-bounded organelle mitochondrial membrane organelle inner membrane membrane mitochondrial inner membrane organelle envelope mitochondrial envelope organelle membrane respiratory chain complex protein-containing complex catalytic complex membrane protein complex transporter complex NADH dehydrogenase complex transmembrane transporter complex respiratory chain complex I oxidoreductase complex
I [auth Z]	NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13-A	-	metabolic process cellular process cellular metabolic compound salvage photorespiration developmental process multicellular organismal process reproductive system development reproductive process embryo development developmental process involved in reproduction multicellular organism development fruit development embryo development ending in seed dormancy seed development metabolic process cellular process cellular metabolic compound salvage photorespiration developmental process multicellular organismal process reproductive system development reproductive process embryo development developmental process involved in reproduction multicellular organism development fruit development embryo development ending in seed dormancy seed development anatomical structure development reproductive structure development post-embryonic development system development	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle mitochondrial membrane organelle inner membrane membrane mitochondrial inner membrane organelle envelope mitochondrial envelope membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle mitochondrial membrane organelle inner membrane membrane mitochondrial inner membrane organelle envelope mitochondrial envelope organelle membrane respiratory chain complex protein-containing complex catalytic complex membrane protein complex transporter complex NADH dehydrogenase complex transmembrane transporter complex respiratory chain complex I oxidoreductase complex extracellular region
J [auth q]	Probable NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12	cation binding transition metal ion binding ion binding binding metal ion binding cobalt ion binding small molecule binding	protein-containing complex organization mitochondrial respirasome assembly NADH dehydrogenase complex assembly cellular component organization cellular component biogenesis organelle organization cellular component assembly mitochondrial respiratory chain complex assembly protein-containing complex assembly cellular process cellular component organization or biogenesis mitochondrial respiratory chain complex I assembly mitochondrion organization	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle intracellular organelle mitochondrion organelle intracellular membrane-bounded organelle mitochondrial membrane organelle inner membrane membrane mitochondrial inner membrane organelle envelope cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle intracellular organelle mitochondrion organelle intracellular membrane-bounded organelle mitochondrial membrane organelle inner membrane membrane mitochondrial inner membrane organelle envelope mitochondrial envelope organelle membrane
G [auth V]	Probable NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5, mitochondrial	-	metabolic process cellular process cellular metabolic compound salvage photorespiration cellular respiration energy derivation by oxidation of organic compounds respiratory electron transport chain electron transport chain generation of precursor metabolites and energy	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle mitochondrial membrane organelle inner membrane membrane mitochondrial inner membrane organelle envelope mitochondrial envelope membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle mitochondrial membrane organelle inner membrane membrane mitochondrial inner membrane organelle envelope mitochondrial envelope organelle membrane respiratory chain complex protein-containing complex catalytic complex membrane protein complex transporter complex NADH dehydrogenase complex transmembrane transporter complex respiratory chain complex I oxidoreductase complex plastid

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth B]	IPR006138	NADH-ubiquinone oxidoreductase, 20 Kd subunit	Family
A [auth B]	IPR006137	NADH:ubiquinone oxidoreductase-like, 20kDa subunit	Domain
B [auth C]	IPR037232	NADH:ubiquinone oxidoreductase, 30kDa subunit superfamily	Homologous Superfamily
B [auth C]	IPR001268	NADH:ubiquinone oxidoreductase, 30kDa subunit	Domain
B [auth C]	IPR020396	NADH:ubiquinone oxidoreductase, 30kDa subunit, conserved site	Conserved Site
B [auth C]	IPR010218	NADH dehydrogenase, subunit C	Family
C [auth D]	IPR022885	NAD(P)H-quinone oxidoreductase subunit D/H	Family
C [auth D]	IPR014029	NADH:ubiquinone oxidoreductase, 49kDa subunit, conserved site	Conserved Site
C [auth D]	IPR029014	[NiFe]-hydrogenase, large subunit	Homologous Superfamily
C [auth D]	IPR001135	NADH-quinone oxidoreductase, subunit D	Domain
D [auth I]	IPR017900	4Fe-4S ferredoxin, iron-sulphur binding, conserved site	Conserved Site
D [auth I]	IPR017896	4Fe-4S ferredoxin-type, iron-sulphur binding domain	Domain
D [auth I]	IPR010226	NADH-quinone oxidoreductase, chain I	Family
E [auth P]	IPR051207	Mitochondrial Complex I NDUFA9 Subunit	Family
E [auth P]	IPR036291	NAD(P)-binding domain superfamily	Homologous Superfamily
E [auth P]	IPR001509	NAD-dependent epimerase/dehydratase	Domain
F [auth U]	IPR006162	Phosphopantetheine attachment site	PTM
F [auth U]	IPR009081	Phosphopantetheine binding ACP domain	Domain
F [auth U]	IPR036736	ACP-like superfamily	Homologous Superfamily
F [auth U]	IPR003231	Acyl carrier protein	Family
H [auth W]	IPR016488	NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex, subunit 6	Family
H [auth W]	IPR045299	NDUFA6, LYR domain	Domain
I [auth Z]	IPR009346	GRIM-19	Family
J [auth q]	IPR007763	NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12	Family
G [auth V]	IPR006806	NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5	Family