8BED

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

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 E]	SCOP2B Superfamily	Thioredoxin-like	8101475	3000031	SCOP2B (2022-06-29)
E [auth Q]	SCOP2B Superfamily	NADH-ubiquinone oxidoreductase-like	8101739	3002258	SCOP2B (2022-06-29)
G [auth S]	SCOP2B Superfamily	Thioredoxin-like	8101737	3000031	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)
B [auth F]	NADH_4Fe-4S	e8bedF1	A: alpha bundles	X: Bromodomain-like	H: Nqo1C-terminal domain-like (From Topology)	T: Nqo1C-terminal domain-like	F: NADH_4Fe-4S	ECOD (1.6)
B [auth F]	SLBB	e8bedF2	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Nqo1 middle domain-like	F: SLBB	ECOD (1.6)
B [auth F]	Complex1_51K	e8bedF3	A: a/b three-layered sandwiches	X: Nqo1 FMN-binding domain-like (From Topology)	H: Nqo1 FMN-binding domain-like (From Topology)	T: Nqo1 FMN-binding domain-like	F: Complex1_51K	ECOD (1.6)
A [auth E]	2Fe-2S_thioredx_N	e8bedE1	A: alpha bundles	X: NQO2 helical bundle domain (From Topology)	H: NQO2 helical bundle domain (From Topology)	T: NQO2 helical bundle domain	F: 2Fe-2S_thioredx_N	ECOD (1.6)
A [auth E]	2Fe-2S_thioredx_C	e8bedE2	A: a+b three layers	X: Thioredoxin-like	H: Thioredoxin-like (From Topology)	T: Thioredoxin-like	F: 2Fe-2S_thioredx_C	ECOD (1.6)
C [auth G]	PRK09129	e8bedG3	A: a+b two layers	X: 4Fe-4S ferredoxin (From Topology)	H: 4Fe-4S ferredoxin (From Topology)	T: 4Fe-4S ferredoxin	F: PRK09129	ECOD (1.6)
C [auth G]	Fer2_4	e8bedG2	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: Fer2_4	ECOD (1.6)
C [auth G]	Molybdop_Fe4S4_1	e8bedG4	A: a+b two layers	X: Formate dehydrogenase/DMSO reductase, domain 1 (From Topology)	H: Formate dehydrogenase/DMSO reductase, domain 1 (From Topology)	T: Formate dehydrogenase/DMSO reductase, domain 1	F: Molybdop_Fe4S4_1	ECOD (1.6)
C [auth G]	Molybdopterin_2nd	e8bedG6	A: a/b three-layered sandwiches	X: Rossmann-like	H: Formate dehydrogenase/DMSO reductase, domains 2 and 3 (From Topology)	T: Formate dehydrogenase/DMSO reductase, domains 2 and 3	F: Molybdopterin_2nd	ECOD (1.6)
C [auth G]	Molybdopterin_1st	e8bedG5	A: a/b three-layered sandwiches	X: Rossmann-like	H: Formate dehydrogenase/DMSO reductase, domains 2 and 3 (From Topology)	T: Formate dehydrogenase/DMSO reductase, domains 2 and 3	F: Molybdopterin_1st	ECOD (1.6)
C [auth G]	NADH-G_4Fe-4S_3	e8bedG1	A: extended segments	X: iron-sulfur center-binding helical hairpin (From Topology)	H: iron-sulfur center-binding helical hairpin (From Topology)	T: iron-sulfur center-binding helical hairpin	F: NADH-G_4Fe-4S_3	ECOD (1.6)
E [auth Q]	ETC_C1_NDUFA4	e8bedQ1	A: a+b two layers	X: Putative oxidoreductase (From Topology)	H: Putative oxidoreductase (From Topology)	T: Putative oxidoreductase	F: ETC_C1_NDUFA4	ECOD (1.6)
F [auth R]	zf-CHCC	e8bedR1	A: few secondary structure elements	X: Rubredoxin-like	H: Rubredoxin-related	T: Cytochrome c oxidase Subunit F	F: zf-CHCC	ECOD (1.6)
G [auth S]	L51_S25_CI-B8	e8bedS1	A: a+b three layers	X: Thioredoxin-like	H: Thioredoxin-like (From Topology)	T: Thioredoxin-like	F: L51_S25_CI-B8	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B [auth F]	PF10531	SLBB domain (SLBB)	SLBB domain	-	Domain
B [auth F]	PF22461	SLBB domain (SLBB_2)	SLBB domain	This entry represents a set of SLBB domains [5].	Domain
B [auth F]	PF01512	Respiratory-chain NADH dehydrogenase 51 Kd subunit (Complex1_51K)	Respiratory-chain NADH dehydrogenase 51 Kd subunit	-	Family
B [auth F]	PF10589	NADH-ubiquinone oxidoreductase-F iron-sulfur binding region (NADH_4Fe-4S)	NADH-ubiquinone oxidoreductase-F iron-sulfur binding region	-	Domain
A [auth E]	PF01257	Thioredoxin-like [2Fe-2S] ferredoxin (2Fe-2S_thioredx)	Thioredoxin-like [2Fe-2S] ferredoxin	-	Family
C [auth G]	PF00384	Molybdopterin oxidoreductase (Molybdopterin)	Molybdopterin oxidoreductase	-	Family
C [auth G]	PF22151	NADH-ubiquinone oxidoreductase NDSU1/NuoG-like, 4Fe-4S domain (NDSU1_4Fe-4S)	NADH-ubiquinone oxidoreductase NDSU1/NuoG-like, 4Fe-4S domain	This entry represents the 4Fe-4S domain of NADH-ubiquinone oxidoreductase NDUFS1 from mammals and NuoG from bacteria, which are part of respiratory chain complex I [1-5].	Domain
C [auth G]	PF09326	NADH-ubiquinone oxidoreductase subunit G, C-terminal (NADH_dhqG_C)	NADH-ubiquinone oxidoreductase subunit G, C-terminal	-	Family
C [auth G]	PF22117	NADH-quinone oxidoreductase subunit 3, ferredoxin-like domain (Nqo3_Fer4)	NADH-quinone oxidoreductase subunit 3, ferredoxin-like domain	NADH-quinone oxidoreductase subunit 3 (Nqo3) is a component of respiratory complex I. This protein is located at the peripheral arm of the complex and consists of multiple domains. This entry represents the second ferredoxin-like domain which contain ...	NADH-quinone oxidoreductase subunit 3 (Nqo3) is a component of respiratory complex I. This protein is located at the peripheral arm of the complex and consists of multiple domains. This entry represents the second ferredoxin-like domain which contains Fe4-S4 cluster, one of the redox centers of the complex [1-5].	Domain
C [auth G]	PF13510	2Fe-2S iron-sulfur cluster binding domain (Fer2_4)	2Fe-2S iron-sulfur cluster binding domain	The 2Fe-2S ferredoxin family have a general core structure consisting of beta(2)-alpha-beta(2) which a beta-grasp type fold. The domain is around one hundred amino acids with four conserved cysteine residues to which the 2Fe-2S cluster is ligated. Th ...	The 2Fe-2S ferredoxin family have a general core structure consisting of beta(2)-alpha-beta(2) which a beta-grasp type fold. The domain is around one hundred amino acids with four conserved cysteine residues to which the 2Fe-2S cluster is ligated. This cluster appears within sarcosine oxidase proteins.	Domain
C [auth G]	PF10588	NADH-ubiquinone oxidoreductase-G iron-sulfur binding region (NADH-G_4Fe-4S_3)	NADH-ubiquinone oxidoreductase-G iron-sulfur binding region	-	Domain
E [auth Q]	PF04800	NADH dehydrogenase ubiquinone Fe-S protein 4 (NDUS4)	NADH dehydrogenase ubiquinone Fe-S protein 4	-	Family
F [auth R]	PF10276	Zinc-finger domain (zf-CHCC)	Zinc-finger domain	This is a short zinc-finger domain conserved from fungi to humans. It is Cx8Hx14Cx2C.	Domain
G [auth S]	PF05047	Mitochondrial ribosomal protein L51 / S25 / CI-B8 domain (L51_S25_CI-B8)	Mitochondrial ribosomal protein L51 / S25 / CI-B8 domain	The proteins in this family are located in the mitochondrion. The family includes ribosomal protein L51, and S25. This family also includes mitochondrial NADH-ubiquinone oxidoreductase B8 subunit (CI-B8) EC:1.6.5.3. It is not known whether all member ...	The proteins in this family are located in the mitochondrion. The family includes ribosomal protein L51, and S25. This family also includes mitochondrial NADH-ubiquinone oxidoreductase B8 subunit (CI-B8) EC:1.6.5.3. It is not known whether all members of this family form part of the NADH-ubiquinone oxidoreductase and whether they are also all ribosomal proteins. Structurally related to thioredoxin-fold.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B [auth F]	NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial	binding nucleotide binding FMN binding nucleoside phosphate binding ion binding organic cyclic compound binding anion binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding monoatomic cation transmembrane transporter activity proton transmembrane transporter activity primary active transmembrane transporter activity binding nucleotide binding FMN binding nucleoside phosphate binding ion binding organic cyclic compound binding anion binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide 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 NAD binding purine nucleotide binding adenyl nucleotide binding iron-sulfur cluster binding 4 iron, 4 sulfur cluster binding metal cluster binding cation binding metal ion binding	-	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle cell periphery plasma membrane membrane
A [auth E]	NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial	iron-sulfur cluster binding 2 iron, 2 sulfur cluster binding binding metal cluster binding small molecule binding cation binding transition metal ion binding zinc ion 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 iron-sulfur cluster binding 2 iron, 2 sulfur cluster binding binding metal cluster binding small molecule binding cation binding transition metal ion binding zinc ion 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	-	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle intracellular organelle mitochondrion organelle intracellular membrane-bounded organelle
C [auth G]	NADH dehydrogenase [ubiquinone] iron-sulfur protein 1, mitochondrial	iron-sulfur cluster binding 2 iron, 2 sulfur cluster binding binding metal cluster 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 iron-sulfur cluster binding 2 iron, 2 sulfur cluster binding binding metal cluster 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 4 iron, 4 sulfur cluster binding cation binding ion binding metal ion binding	metabolic process cellular process cellular metabolic compound salvage photorespiration aerobic respiration cellular respiration oxidative phosphorylation energy derivation by oxidation of organic compounds respiratory electron transport chain ATP synthesis coupled electron transport 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 plastid mitochondrial membrane membrane organelle envelope mitochondrial envelope organelle membrane membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle plastid mitochondrial membrane 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 chloroplast
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
E [auth Q]	NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial	cation binding transition metal ion binding ion binding binding metal ion binding cobalt ion 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 cation binding transition metal ion binding ion binding binding metal ion binding cobalt ion 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	electron transport chain metabolic process cellular process generation of precursor metabolites and energy response to stimulus cold acclimation response to stress response to abiotic stimulus response to cold response to temperature stimulus response to osmotic stress	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle plastid
F [auth R]	NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial	-	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
G [auth S]	NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2	-	-	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle plastid
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

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B [auth F]	IPR019575	NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain	Domain
B [auth F]	IPR011537	NADH ubiquinone oxidoreductase, F subunit	Family
B [auth F]	IPR001949	NADH:ubiquinone oxidoreductase, 51kDa subunit, conserved site	Conserved Site
B [auth F]	IPR037225	NADH-ubiquinone oxidoreductase 51kDa subunit, FMN-binding domain superfamily	Homologous Superfamily
B [auth F]	IPR037207	NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain superfamily	Homologous Superfamily
B [auth F]	IPR011538	NADH-ubiquinone oxidoreductase 51kDa subunit, FMN-binding domain	Domain
B [auth F]	IPR050837	Complex I 51 kDa subunit	Family
A [auth E]	IPR042128	NuoE domain	Domain
A [auth E]	IPR002023	NADH-quinone oxidoreductase subunit E-like	Family
A [auth E]	IPR041921	NADH-quinone oxidoreductase subunit E, N-terminal	Homologous Superfamily
A [auth E]	IPR036249	Thioredoxin-like superfamily	Homologous Superfamily
C [auth G]	IPR006963	Molybdopterin oxidoreductase, 4Fe-4S domain	Domain
C [auth G]	IPR015405	NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial-like	Domain
C [auth G]	IPR006656	Molybdopterin oxidoreductase	Domain
C [auth G]	IPR036010	2Fe-2S ferredoxin-like superfamily	Homologous Superfamily
C [auth G]	IPR001041	2Fe-2S ferredoxin-type iron-sulfur binding domain	Domain
C [auth G]	IPR000283	NADH:ubiquinone oxidoreductase, 75kDa subunit, conserved site	Conserved Site
C [auth G]	IPR054351	NADH-ubiquinone oxidoreductase, ferredoxin-like domain	Domain
C [auth G]	IPR010228	NADH:ubiquinone oxidoreductase, subunit G	Family
C [auth G]	IPR050123	Prokaryotic molybdopterin-containing oxidoreductase	Family
C [auth G]	IPR019574	NADH:ubiquinone oxidoreductase, subunit G, iron-sulphur binding	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 Q]	IPR038532	NADH dehydrogenase ubiquinone Fe-S protein 4-like superfamily	Homologous Superfamily
E [auth Q]	IPR006885	NADH dehydrogenase ubiquinone Fe-S protein 4 mitochondrial-like	Family
F [auth R]	IPR019401	Zinc finger, CHCC-type	Domain
F [auth R]	IPR016668	NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial	Family
G [auth S]	IPR007741	Ribosomal protein/NADH dehydrogenase domain	Domain
G [auth S]	IPR036249	Thioredoxin-like superfamily	Homologous Superfamily
G [auth S]	IPR016464	NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex, subunit 2	Family
H [auth W]	IPR016488	NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex, subunit 6	Family
H [auth W]	IPR045299	NDUFA6, LYR domain	Domain