6HWH | pdb_00006hwh

Structure of a functional obligate respiratory supercomplex from Mycobacterium smegmatis

External Resource: Annotation

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

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
J [auth V]	SCOP2 Family	Cytochrome c oxidase subunit I-like	8097007	4001989	SCOP2 (2022-06-29)
J [auth V]	SCOP2 Superfamily	Cytochrome c oxidase subunit I-like	8097008	3000653	SCOP2 (2022-06-29)
W [auth Q]	SCOP2B Superfamily	Cytochrome c oxidase subunit I-like	8097008	3000653	SCOP2B (2022-06-29)
Y [auth W]	SCOP2 Family	Cytochrome c oxidase subunit III-like	8075785	4002000	SCOP2 (2022-06-29)
Y [auth W]	SCOP2 Superfamily	Cytochrome c oxidase subunit III-like	8075786	3000671	SCOP2 (2022-06-29)
L [auth Z]	SCOP2B Superfamily	Cytochrome c oxidase subunit III-like	8075786	3000671	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)
G [auth P]	Ribosomal_L1	e6hwhP1	A: a/b three-layered sandwiches	X: PriB N-terminal domain-like	H: HTH	T: SH3	F: Ribosomal_L1	ECOD (v294.1)
T [auth L]	Ribosomal_L1	e6hwhL1	A: a/b three-layered sandwiches	X: PriB N-terminal domain-like	H: HTH	T: SH3	F: Ribosomal_L1	ECOD (v294.1)
I [auth T]	RRM_1	e6hwhT1	A: a/b three-layered sandwiches	X: PriB N-terminal domain-like	H: HTH	T: SH3	F: RRM_1	ECOD (v294.1)
V [auth O]	Ribosomal_L1	e6hwhO1	A: a/b three-layered sandwiches	X: PriB N-terminal domain-like	H: HTH	T: SH3	F: Ribosomal_L1	ECOD (v294.1)
J [auth V]	RRM_1	e6hwhV1	A: a/b three-layered sandwiches	X: PriB N-terminal domain-like	H: HTH	T: SH3	F: RRM_1	ECOD (v294.1)
W [auth Q]	Ribosomal_L1	e6hwhQ1	A: a/b three-layered sandwiches	X: PriB N-terminal domain-like	H: HTH	T: SH3	F: Ribosomal_L1	ECOD (v294.1)
M [auth b]	PSI_PsaH	e6hwhb01	A: a/b three-layered sandwiches	X: Rossmann-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: PSI_PsaH	ECOD (v294.1)
BA [auth j]	Ribosomal_L1	e6hwhj1	A: a/b three-layered sandwiches	X: PriB N-terminal domain-like	H: HTH	T: SH3	F: Ribosomal_L1	ECOD (v294.1)
AA [auth i]	Cytochrom_C	e6hwhi1	A: a/b three-layered sandwiches	X: PriB N-terminal domain-like	H: HTH	T: SH3	F: Cytochrom_C	ECOD (v294.1)
Y [auth W]	Ribosomal_L1	e6hwhW1	A: a/b three-layered sandwiches	X: PriB N-terminal domain-like	H: HTH	T: SH3	F: Ribosomal_L1	ECOD (v294.1)
L [auth Z]	RRM_1	e6hwhZ1	A: a/b three-layered sandwiches	X: PriB N-terminal domain-like	H: HTH	T: SH3	F: RRM_1	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
J [auth V]	1.20.210.10	Mainly Alpha	Up-down Bundle	Cytochrome C Oxidase	Chain A	CATH (utative)
W [auth Q]	1.20.210.10	Mainly Alpha	Up-down Bundle	Cytochrome C Oxidase	Chain A	CATH (utative)
Z [auth Y]	1.20.810.10	Mainly Alpha	Up-down Bundle	Cytochrome Bc1 Complex	Chain C	CATH (utative)
M [auth b]	1.20.810.10	Mainly Alpha	Up-down Bundle	Cytochrome Bc1 Complex	Chain C	CATH (utative)
Y [auth W]	1.20.120.80	Mainly Alpha	Up-down Bundle	Four Helix Bundle (Hemerythrin (Met), subunit A)	Cytochrome c oxidase, subunit III, four-helix bundle	CATH (utative)
L [auth Z]	1.20.120.80	Mainly Alpha	Up-down Bundle	Four Helix Bundle (Hemerythrin (Met), subunit A)	Cytochrome c oxidase, subunit III, four-helix bundle	CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, N [auth B]	PF13631	Cytochrome b(N-terminal)/b6/petB (Cytochrom_B_N_2)	Cytochrome b(N-terminal)/b6/petB		Domain
A, N [auth B]	PF00355	Rieske [2Fe-2S] domain (Rieske)	Rieske [2Fe-2S] domain	The rieske domain has a [2Fe-2S] centre. Two conserved cysteines coordinate one Fe ion, while the other Fe ion is coordinated by two conserved histidines. In hyperthermophilic archaea there is a SKTPCX(2-3)C motif at the C-terminus. The cysteines in ...	The rieske domain has a [2Fe-2S] centre. Two conserved cysteines coordinate one Fe ion, while the other Fe ion is coordinated by two conserved histidines. In hyperthermophilic archaea there is a SKTPCX(2-3)C motif at the C-terminus. The cysteines in this motif form a disulphide bridge, which stabilises the protein [4].	Domain
I [auth T], V [auth O]	PF17174	Domain of unknown function (DUF5130) (DUF5130)	Domain of unknown function (DUF5130)	-	Family
J [auth V], W [auth Q]	PF00115	Cytochrome C and Quinol oxidase polypeptide I (COX1)	Cytochrome C and Quinol oxidase polypeptide I	-	Family
K [auth X], X [auth S]	PF12270	Cytochrome c oxidase subunit IV (Cyt_c_ox_IV)	Cytochrome c oxidase subunit IV	-	Family
M [auth b], Z [auth Y]	PF13631	Cytochrome b(N-terminal)/b6/petB (Cytochrom_B_N_2)	Cytochrome b(N-terminal)/b6/petB		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, N [auth B]	Ubiquinol-cytochrome c reductase iron-sulfur subunit	monooxygenase activity oxidoreductase activity catalytic activity oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen iron-sulfur cluster binding 2 iron, 2 sulfur cluster binding binding metal cluster binding small molecule binding cation binding ion binding metal ion binding	-	cell periphery cellular anatomical structure plasma membrane membrane
B [auth G], O [auth C]	Co-purified unknown transmembrane helices built as polyALA	-	-	-
C [auth H], P [auth D]	Co-purified unknown transmembrane helices built as polyALA	-	-	-
D [auth I], Q [auth E]	Co-purified unknown peptide built as polyALA	-	-	-
E [auth J], R [auth F]	Co-purified unknown peptide built as polyALA	-	-	-
G [auth P], T [auth L]	Cytochrome c oxidase subunit 2	oxidoreductase activity catalytic activity cation binding transition metal ion binding copper ion binding ion binding binding metal ion binding small molecule binding monoatomic cation transmembrane transporter activity proton transmembrane transporter activity primary active transmembrane transporter activity cytochrome-c oxidase activity electron transfer activity oxidoreductase activity catalytic activity cation binding transition metal ion binding copper ion binding ion binding binding metal ion binding small molecule binding monoatomic cation transmembrane transporter activity proton transmembrane transporter activity primary active transmembrane transporter activity cytochrome-c oxidase activity electron transfer activity active monoatomic ion transmembrane transporter activity oxidoreduction-driven active transmembrane transporter activity active transmembrane transporter activity monoatomic ion transmembrane transporter activity transporter activity transmembrane transporter activity	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 metabolic process cellular process generation of precursor metabolites and energy	cellular anatomical structure membrane
I [auth T], V [auth O]	Uncharacterized protein MSMEG_4692/MSMEI_4575	-	-	-
J [auth V], W [auth Q]	Cytochrome c oxidase subunit 1	oxidoreductase activity catalytic activity monoatomic cation transmembrane transporter activity proton transmembrane transporter activity primary active transmembrane transporter activity cytochrome-c oxidase activity electron transfer activity active monoatomic ion transmembrane transporter 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 cytochrome-c oxidase activity electron transfer activity active monoatomic ion transmembrane transporter activity oxidoreduction-driven active transmembrane transporter activity active transmembrane transporter activity monoatomic ion transmembrane transporter activity transporter activity transmembrane transporter activity binding tetrapyrrole binding heme binding cation binding ion binding metal ion binding small molecule 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 oxidative phosphorylation energy derivation by oxidation of organic compounds metabolic process generation of precursor metabolites and energy respiratory electron transport chain electron transport chain	cell periphery cellular anatomical structure plasma membrane membrane
K [auth X], X [auth S]	Cytochrome c oxidase polypeptide 4	oxidoreductase activity catalytic activity monoatomic cation transmembrane transporter activity proton transmembrane transporter activity primary active transmembrane transporter activity cytochrome-c oxidase activity electron transfer activity active monoatomic ion transmembrane transporter activity oxidoreduction-driven active transmembrane transporter activity active transmembrane transporter activity monoatomic ion transmembrane transporter activity transporter activity transmembrane transporter activity	electron transport chain metabolic process cellular process generation of precursor metabolites and energy	cell periphery cellular anatomical structure plasma membrane membrane
M [auth b], Z [auth Y]	Ubiquinol-cytochrome C reductase QcrB	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 oxidoreduction-driven active transmembrane transporter activity active transmembrane transporter activity quinol-cytochrome-c reductase activity monoatomic ion transmembrane transporter activity transporter activity transmembrane transporter activity cation 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 oxidoreduction-driven active transmembrane transporter activity active transmembrane transporter activity quinol-cytochrome-c reductase activity monoatomic ion transmembrane transporter activity transporter activity transmembrane transporter activity cation binding ion binding binding metal ion binding small molecule binding	cellular respiration energy derivation by oxidation of organic compounds respiratory electron transport chain electron transport chain metabolic process cellular process generation of precursor metabolites and energy	cell periphery cellular anatomical structure plasma membrane membrane
H [auth R], U [auth N]	MSMEG_4693	-	-	-
AA [auth i], BA [auth j], F [auth M], S [auth K]	Cytochrome bc1 complex cytochrome c subunit	monoatomic cation transmembrane transporter activity proton transmembrane transporter activity primary active transmembrane transporter activity electron transfer activity active monoatomic ion transmembrane transporter activity oxidoreduction-driven active transmembrane transporter activity active transmembrane transporter activity quinol-cytochrome-c reductase activity monoatomic ion transmembrane transporter activity transporter activity transmembrane transporter activity binding tetrapyrrole binding heme binding monoatomic cation transmembrane transporter activity proton transmembrane transporter activity primary active transmembrane transporter activity electron transfer activity active monoatomic ion transmembrane transporter activity oxidoreduction-driven active transmembrane transporter activity active transmembrane transporter activity quinol-cytochrome-c reductase activity monoatomic ion transmembrane transporter activity transporter activity transmembrane transporter activity binding tetrapyrrole binding heme binding cation binding transition metal ion binding iron ion binding ion binding metal ion binding small molecule binding	-	cell periphery cellular anatomical structure plasma membrane membrane
L [auth Z], Y [auth W]	Cytochrome c oxidase subunit 3	oxidoreductase activity catalytic activity monoatomic cation transmembrane transporter activity proton transmembrane transporter activity primary active transmembrane transporter activity cytochrome-c oxidase activity electron transfer activity active monoatomic ion transmembrane transporter activity oxidoreduction-driven active transmembrane transporter activity active transmembrane transporter activity monoatomic ion transmembrane transporter activity transporter activity transmembrane transporter activity	aerobic electron transport chain aerobic respiration cellular respiration oxidative phosphorylation energy derivation by oxidation of organic compounds respiratory electron transport chain electron transport chain metabolic process cellular process generation of precursor metabolites and energy	cell periphery cellular anatomical structure plasma membrane membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, N [auth B]	IPR017941	Rieske [2Fe-2S] iron-sulphur domain	Domain
A, N [auth B]	IPR045603	QcrA subunit, N-terminal	Domain
A, N [auth B]	IPR036922	Rieske [2Fe-2S] iron-sulphur domain superfamily	Homologous Superfamily
A, N [auth B]	IPR014349	Rieske iron-sulphur protein	Family
G [auth P], T [auth L]	IPR002429	Cytochrome c oxidase subunit II-like C-terminal	Domain
G [auth P], T [auth L]	IPR036257	Cytochrome C oxidase subunit II, transmembrane domain superfamily	Homologous Superfamily
G [auth P], T [auth L]	IPR008972	Cupredoxin	Homologous Superfamily
G [auth P], T [auth L]	IPR001505	Copper centre Cu(A)	Binding Site
G [auth P], T [auth L]	IPR045187	Cytochrome c/quinol oxidase subunit II	Family
I [auth T], V [auth O]	IPR033437	Protein of unknown function DUF5130	Family
J [auth V], W [auth Q]	IPR036927	Cytochrome c oxidase-like, subunit I superfamily	Homologous Superfamily
J [auth V], W [auth Q]	IPR000883	Cytochrome c oxidase subunit I	Family
J [auth V], W [auth Q]	IPR023615	Cytochrome c oxidase, subunit I, copper-binding site	Binding Site
J [auth V], W [auth Q]	IPR023616	Cytochrome c oxidase-like, subunit I domain	Domain
J [auth V], W [auth Q]	IPR014241	Cytochrome c oxidase, subunit I bacterial type	Family
K [auth X], X [auth S]	IPR021050	Cytochrome c oxidase subunit IV, actinobacteria	Family
M [auth b], Z [auth Y]	IPR027387	Cytochrome b/b6-like domain superfamily	Homologous Superfamily
M [auth b], Z [auth Y]	IPR016174	Di-haem cytochrome, transmembrane	Homologous Superfamily
M [auth b], Z [auth Y]	IPR005797	Cytochrome b/b6, N-terminal domain	Domain
AA [auth i], BA [auth j], F [auth M], S [auth K]	IPR009152	Cytochrome bc1 complex, cytochrome c subunit	Family
AA [auth i], BA [auth j], F [auth M], S [auth K]	IPR036909	Cytochrome c-like domain superfamily	Homologous Superfamily
AA [auth i], BA [auth j], F [auth M], S [auth K]	IPR050597	Cytochrome c Oxidase Subunit	Family
AA [auth i], BA [auth j], F [auth M], S [auth K]	IPR009056	Cytochrome c-like domain	Domain
L [auth Z], Y [auth W]	IPR035973	Cytochrome c oxidase subunit III-like superfamily	Homologous Superfamily
L [auth Z], Y [auth W]	IPR013833	Cytochrome c oxidase, subunit III, 4-helical bundle	Homologous Superfamily
L [auth Z], Y [auth W]	IPR000298	Cytochrome c oxidase subunit III-like	Domain
L [auth Z], Y [auth W]	IPR024791	Cytochrome c oxidase subunit III	Family

Membrane Protein Annotation: OPM OPM Database Homepage

Chains	External Link	Type	Class	Superfamily	Family
A, AA [auth i], BA [auth j], F [auth M], G [auth P] A, AA [auth i], BA [auth j], F [auth M], G [auth P], H [auth R], J [auth V], K [auth X], L [auth Z], M [auth b], N [auth B], S [auth K], T [auth L], U [auth N], W [auth Q], X [auth S], Y [auth W], Z [auth Y]	OPM	Transmembrane	Alpha-helical polytopic	Electron transport chain complex IV (cytochrome c oxidase)	Respiratory supercomplexes III-IV

Membrane Protein Annotation: PDBTM PDBTM Database Homepage

Chains	External Link	Comment
A, AA [auth i], BA [auth j], F [auth M], G [auth P] A, AA [auth i], BA [auth j], F [auth M], G [auth P], H [auth R], J [auth V], K [auth X], L [auth Z], M [auth b], N [auth B], S [auth K], T [auth L], U [auth N], W [auth Q], X [auth S], Y [auth W], Z [auth Y]	PDBTM	Annotated as membrane protein by PDBTM

Membrane Protein Annotation: mpstruc mpstruc Database Homepage

Chains	Resource Link	Group	Subgroup	Protein
A, AA [auth i], BA [auth j], F [auth M], G [auth P] A, AA [auth i], BA [auth j], F [auth M], G [auth P], H [auth R], J [auth V], K [auth X], L [auth Z], M [auth b], N [auth B], S [auth K], T [auth L], U [auth N], W [auth Q], X [auth S], Y [auth W], Z [auth Y]	mpstruc	TRANSMEMBRANE PROTEINS: ALPHA-HELICAL	Electron Transport Chain Supercomplexes (Respirasome)	Respiratory supercomplex CIII₂CIV₂