8BEE | pdb_00008bee

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

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: mpstruc

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
F [auth U]	SCOP2B Superfamily	ACP-like	8101483	3001805	SCOP2B (2022-06-29)
C [auth D]	SCOP2B Superfamily	HydB/Nqo4-like	8101589	3001849	SCOP2B (2022-06-29)
A [auth B]	SCOP2B Superfamily	Nqo6/HydA N-terminal domain-like	8101623	3002291	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)
H [auth W]	PAE	e8beeW1	A: alpha bundles	X: RNase A-like	H: Cytochrome P450	T: Cytochrome P450	F: PAE	ECOD (develop294)
F [auth U]	PAE	e8beeU1	A: alpha bundles	X: RNase A-like	H: Cytochrome P450	T: Cytochrome P450	F: PAE	ECOD (develop294)
E [auth P]	PAE	e8beeP1	A: alpha bundles	X: RNase A-like	H: Cytochrome P450	T: Cytochrome P450	F: PAE	ECOD (develop294)
D [auth I]	PAE	e8beeI1	A: alpha bundles	X: RNase A-like	H: Cytochrome P450	T: Cytochrome P450	F: PAE	ECOD (develop294)
C [auth D]	PAE	e8beeD1	A: alpha bundles	X: RNase A-like	H: Cytochrome P450	T: Cytochrome P450	F: PAE	ECOD (develop294)
B [auth C]	PAE	e8beeC1	A: alpha bundles	X: RNase A-like	H: Cytochrome P450	T: Cytochrome P450	F: PAE	ECOD (develop294)
J [auth q]	PAE	e8beeq1	A: alpha bundles	X: RNase A-like	H: Cytochrome P450	T: Cytochrome P450	F: PAE	ECOD (develop294)
A [auth B]	PAE	e8beeB1	A: alpha bundles	X: RNase A-like	H: Cytochrome P450	T: Cytochrome P450	F: PAE	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
C [auth D]	1.10.645.10	Mainly Alpha	Orthogonal Bundle	Cytochrome-c3 Hydrogenase	chain B	CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
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
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
E [auth P]	PF01370	NAD dependent epimerase/dehydratase family (Epimerase)	NAD dependent epimerase/dehydratase family	-	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
C [auth D]	PF00346	Respiratory-chain NADH dehydrogenase, 49 Kd subunit (Complex1_49kDa)	Respiratory-chain NADH dehydrogenase, 49 Kd subunit	-	Family
B [auth C]	PF00329	Respiratory-chain NADH dehydrogenase, 30 Kd subunit (Complex1_30kDa)	Respiratory-chain NADH dehydrogenase, 30 Kd subunit		Domain
A [auth B]	PF01058	NADH ubiquinone oxidoreductase, 20 Kd subunit (Oxidored_q6)	NADH ubiquinone oxidoreductase, 20 Kd subunit		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
I [auth Z]	NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13-A	-	metabolic compound salvage biosynthetic process metabolic process cellular process 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 metabolic compound salvage biosynthetic process metabolic process cellular process 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
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
G [auth V]	Probable NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5, mitochondrial	-	metabolic compound salvage biosynthetic process metabolic process cellular process 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
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 acyl binding	monoatomic cation transmembrane transport transmembrane transport localization transport proton transmembrane transport monoatomic ion transmembrane transport monoatomic ion transport cellular process monoatomic cation transport establishment of localization aerobic respiration cellular respiration aerobic electron transport chain oxidative phosphorylation monoatomic cation transmembrane transport transmembrane transport localization transport proton transmembrane transport monoatomic ion transmembrane transport monoatomic ion transport cellular process monoatomic cation transport establishment of localization 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 respiratory chain complex protein-containing complex catalytic complex membrane membrane protein complex membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle cytosol 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 membrane-enclosed lumen mitochondrial matrix intracellular organelle lumen organelle lumen nucleus
E [auth P]	NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mitochondrial	protein-containing complex binding binding	small molecule biosynthetic process ketone metabolic process ubiquinone biosynthetic process quinone metabolic process biosynthetic process quinone biosynthetic process metabolic process cellular process small molecule metabolic process ubiquinone metabolic process ketone biosynthetic process	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 membrane-enclosed lumen mitochondrial matrix intracellular organelle lumen organelle lumen
D [auth I]	NADH dehydrogenase [ubiquinone] iron-sulfur protein 8-A, mitochondrial	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 cation binding ion binding metal ion binding monoatomic cation transmembrane transporter activity proton transmembrane transporter activity primary active transmembrane transporter activity 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 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	protein-containing complex organization 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 aerobic respiration cellular respiration protein-containing complex organization 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 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 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
C [auth D]	NADH dehydrogenase subunit 7	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 monoatomic cation transmembrane transporter activity proton transmembrane transporter activity primary active transmembrane transporter activity 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 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	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 plastid
B [auth C]	NADH dehydrogenase [ubiquinone] iron-sulfur protein 3	cation binding transition metal ion binding ion binding binding metal ion binding cobalt ion binding small molecule binding zinc ion binding oxidoreductase activity oxidoreductase activity, acting on NAD(P)H catalytic activity monoatomic cation transmembrane transporter activity proton transmembrane transporter activity primary active transmembrane transporter activity cation binding transition metal ion binding ion binding binding metal ion binding cobalt ion binding small molecule binding zinc ion binding oxidoreductase activity oxidoreductase activity, acting on NAD(P)H catalytic activity 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	-	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
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	-	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
A [auth B]	NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial	oxidoreductase activity catalytic activity 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 binding oxidoreductase activity catalytic activity 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 binding quinone binding small molecule binding cation binding transition metal ion binding zinc ion binding ion binding metal ion binding iron-sulfur cluster binding 4 iron, 4 sulfur cluster binding metal cluster 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 protein-containing complex organization 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 component organization or biogenesis mitochondrial respiratory chain complex I assembly mitochondrion organization	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 cell periphery plasma membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
I [auth Z]	IPR009346	GRIM-19	Family
H [auth W]	IPR016488	NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex, subunit 6	Family
H [auth W]	IPR045299	NDUFA6, LYR domain	Domain
G [auth V]	IPR006806	NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5	Family
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
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
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
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
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
J [auth q]	IPR007763	NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12	Family
A [auth B]	IPR006137	NADH:ubiquinone oxidoreductase-like, 20kDa subunit	Domain
A [auth B]	IPR006138	NADH-ubiquinone oxidoreductase, 20 Kd subunit	Family

Membrane Protein Annotation: mpstruc mpstruc Database Homepage

Chains	Resource Link	Group	Subgroup	Protein
A [auth B], B [auth C], D [auth I], E [auth P], F [auth U] A [auth B], B [auth C], D [auth I], E [auth P], F [auth U], G [auth V], H [auth W], I [auth Z], J [auth q]	mpstruc	TRANSMEMBRANE PROTEINS: ALPHA-HELICAL	Electron Transport Chain Supercomplexes (Respirasome)	Respiratory supercomplex I-III₂, Complete composition