3RKO | pdb_00003rko

Crystal structure of the membrane domain of respiratory complex I from E. coli at 3.0 angstrom resolution

External Resource: Annotation

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

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
F [auth J]	d3rkoj_	Membrane and cell surface proteins and peptides	Non-antiporter membrane subunits from respiratory complex I	Respiratory complex I subunit NuoJ-like	Respiratory complex I subunit NuoJ-like	NADH-quinone oxidoreductase subunit J, NuoJ/Nqo10	(Escherichia coli BL21(DE3) ) [TaxId: 469008 ],	SCOPe (2.08)
K [auth E]	d3rkoe_	Membrane and cell surface proteins and peptides	Non-antiporter membrane subunits from respiratory complex I	Respiratory complex I subunit NuoA-like	Respiratory complex I subunit NuoA-like	automated matches	(Escherichia coli BL21(DE3) ) [TaxId: 469008 ],	SCOPe (2.08)
E [auth A]	d3rkoa_	Membrane and cell surface proteins and peptides	Non-antiporter membrane subunits from respiratory complex I	Respiratory complex I subunit NuoA-like	Respiratory complex I subunit NuoA-like	NADH-quinone oxidoreductase subunit A, NuoA/Nqo7	(Escherichia coli BL21(DE3) ) [TaxId: 469008 ],	SCOPe (2.08)
J [auth G]	d3rkog_	Membrane and cell surface proteins and peptides	Non-antiporter membrane subunits from respiratory complex I	Respiratory complex I subunit NuoK-like	Respiratory complex I subunit NuoK-like	automated matches	(Escherichia coli BL21(DE3) ) [TaxId: 469008 ],	SCOPe (2.08)
D [auth K]	d3rkok_	Membrane and cell surface proteins and peptides	Non-antiporter membrane subunits from respiratory complex I	Respiratory complex I subunit NuoK-like	Respiratory complex I subunit NuoK-like	NADH-quinone oxidoreductase subunit K, NuoK/Nqo11	(Escherichia coli BL21(DE3) ) [TaxId: 469008 ],	SCOPe (2.08)
I [auth D]	d3rkod_	Membrane and cell surface proteins and peptides	Antiporter-like subunits from respiratory complex I	Antiporter-like subunits from respiratory complex I	Double antiporter-like subunits from respiratory complex I	automated matches	(Escherichia coli BL21(DE3) ) [TaxId: 469008 ],	SCOPe (2.08)
C [auth N]	d3rkon_	Membrane and cell surface proteins and peptides	Antiporter-like subunits from respiratory complex I	Antiporter-like subunits from respiratory complex I	Double antiporter-like subunits from respiratory complex I	NADH-quinone oxidoreductase subunit N, NuoN/Nqo14	(Escherichia coli BL21(DE3) ) [TaxId: 469008 ],	SCOPe (2.08)
H [auth C]	d3rkoc_	Membrane and cell surface proteins and peptides	Antiporter-like subunits from respiratory complex I	Antiporter-like subunits from respiratory complex I	Double antiporter-like subunits from respiratory complex I	automated matches	(Escherichia coli BL21(DE3) ) [TaxId: 469008 ],	SCOPe (2.08)
B [auth M]	d3rkom_	Membrane and cell surface proteins and peptides	Antiporter-like subunits from respiratory complex I	Antiporter-like subunits from respiratory complex I	Double antiporter-like subunits from respiratory complex I	NADH-quinone oxidoreductase subunit M, NuoM/Nqo13	(Escherichia coli BL21(DE3) ) [TaxId: 469008 ],	SCOPe (2.08)
A [auth L]	d3rkol_	Membrane and cell surface proteins and peptides	Antiporter-like subunits from respiratory complex I	Antiporter-like subunits from respiratory complex I	Double antiporter-like subunits from respiratory complex I	NADH-quinone oxidoreductase subunit L, NuoL/Nqo12	(Escherichia coli BL21(DE3) ) [TaxId: 469008 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
L [auth F]	SCOP2 Family	NADH-quinone oxidoreductase NDH subunit 10-like	8085750	4005844	SCOP2 (2022-06-29)
L [auth F]	SCOP2 Superfamily	NADH-quinone oxidoreductase, subunit 11-like	8085751	3002200	SCOP2 (2022-06-29)
E [auth A]	SCOP2 Family	NADH-ubiquinone oxidoreductase chain 3-like	8067559	4005842	SCOP2 (2022-06-29)
E [auth A]	SCOP2 Superfamily	NADH-quinone oxidoreductase, subunit 11-like	8106706	3002200	SCOP2 (2022-06-29)
J [auth G]	SCOP2B Superfamily	NADH-quinone oxidoreductase, subunit 11-like	8053513	3002200	SCOP2B (2022-06-29)
D [auth K]	SCOP2 Family	NADH-quinone oxidoreductase NDH subunit 11-like	8047740	4005793	SCOP2 (2022-06-29)
D [auth K]	SCOP2 Superfamily	NADH-quinone oxidoreductase, subunit 11-like	8053513	3002200	SCOP2 (2022-06-29)
C [auth N]	SCOP2 Family	ND4 antiporter-like subunits	8054171	4005749	SCOP2 (2022-06-29)
C [auth N]	SCOP2 Superfamily	Antiporter subunits half-channel-like	8054173	3002280	SCOP2 (2022-06-29)
C [auth N]	SCOP2 Superfamily	Antiporter subunits half-channel-like	8054172	3002280	SCOP2 (2022-06-29)
B [auth M]	SCOP2 Family	ND4 antiporter-like subunits	8054168	4005749	SCOP2 (2022-06-29)
B [auth M]	SCOP2 Superfamily	Antiporter subunits half-channel-like	8054169	3002280	SCOP2 (2022-06-29)
B [auth M]	SCOP2 Superfamily	Antiporter subunits half-channel-like	8054170	3002280	SCOP2 (2022-06-29)
A [auth L]	SCOP2 Family	ND5 antiporter-like subunits	8054166	4005931	SCOP2 (2022-06-29)
A [auth L]	SCOP2 Superfamily	Antiporter subunits half-channel-like	8054167	3002280	SCOP2 (2022-06-29)
A [auth L]	SCOP2 Superfamily	Antiporter subunits half-channel-like	8054165	3002280	SCOP2 (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
L [auth F]	FeoB_Cyto	e3rkoF1	A: alpha bundles	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: FeoB_Cyto	ECOD (develop294)
F [auth J]	Oxidored_q3	e3rkoJ1	A: alpha bundles	X: NADH-quinone oxidoreductase subunit J	H: NADH-quinone oxidoreductase subunit J	T: NADH-quinone oxidoreductase subunit J	F: Oxidored_q3	ECOD (develop294)
K [auth E]	FeoB_Cyto	e3rkoE1	A: alpha bundles	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: FeoB_Cyto	ECOD (develop294)
E [auth A]	Oxidored_q4	e3rkoA1	A: alpha bundles	X: Cysteine proteinases-like	H: Cysteine proteinases	T: Cysteine proteinases	F: Oxidored_q4	ECOD (develop294)
J [auth G]	FeoB_Cyto	e3rkoG1	A: alpha bundles	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: FeoB_Cyto	ECOD (develop294)
D [auth K]	LPMO_10	e3rkoK1	A: alpha bundles	X: Hormone receptor domain (HRM, Pfam 02793)	H: Hormone receptor domain (HRM, Pfam 02793)	T: Hormone receptor domain (HRM, Pfam 02793)	F: LPMO_10	ECOD (develop294)
I [auth D]	Gal-bind_lectin	e3rkoD1	A: alpha bundles	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Gal-bind_lectin	ECOD (develop294)
C [auth N]	Gal-bind_lectin	e3rkoN1	A: alpha bundles	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Gal-bind_lectin	ECOD (develop294)
H [auth C]	Ribosomal_S6e	e3rkoC1	A: alpha bundles	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: Ribosomal_S6e	ECOD (develop294)
B [auth M]	Ribosomal_S6e	e3rkoM1	A: alpha bundles	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: Ribosomal_S6e	ECOD (develop294)
A [auth L]	Proton_antipo_M,Proton_antipo_N	e3rkoL1	A: alpha bundles	X: Sodium/proton antiporter subunits-like	H: Sodium/proton antiporter subunits-like	T: NADH-quinone oxidoreductase subunit L (NuoL)-related	F: Proton_antipo_M,Proton_antipo_N	ECOD (develop294)
G [auth B]	FeoB_Cyto	e3rkoB1	A: alpha bundles	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: FeoB_Cyto	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
L [auth F]	1.20.120.1200	Mainly Alpha	Up-down Bundle	Four Helix Bundle (Hemerythrin (Met), subunit A)	NADH-ubiquinone/plastoquinone oxidoreductase chain 6, subunit NuoJ	CATH (4.3.0)
F [auth J]	1.20.120.1200	Mainly Alpha	Up-down Bundle	Four Helix Bundle (Hemerythrin (Met), subunit A)	NADH-ubiquinone/plastoquinone oxidoreductase chain 6, subunit NuoJ	CATH (4.3.0)
K [auth E]	1.20.58.1610	Mainly Alpha	Up-down Bundle	Methane Monooxygenase Hydroxylase	Chain G, domain 1	CATH (4.3.0)
E [auth A]	1.20.58.1610	Mainly Alpha	Up-down Bundle	Methane Monooxygenase Hydroxylase	Chain G, domain 1	CATH (4.3.0)
J [auth G]	1.10.287.3510	Mainly Alpha	Orthogonal Bundle	Helix Hairpins		CATH (4.3.0)
D [auth K]	1.10.287.3510	Mainly Alpha	Orthogonal Bundle	Helix Hairpins		CATH (4.3.0)
A [auth L]	1.20.5.2700	Mainly Alpha	Up-down Bundle	Single alpha-helices involved in coiled-coils or other helix-helix interfaces		CATH (4.3.0)
G [auth B]	1.20.5.2700	Mainly Alpha	Up-down Bundle	Single alpha-helices involved in coiled-coils or other helix-helix interfaces		CATH (4.3.0)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
F [auth J], L [auth F]	NADH-QUINONE OXIDOREDUCTASE SUBUNIT J	-	-	-
E [auth A], K [auth E]	NADH-QUINONE OXIDOREDUCTASE SUBUNIT A	-	-	-
D [auth K], J [auth G]	NADH-QUINONE OXIDOREDUCTASE SUBUNIT K	oxidoreductase activity NAD(P)H dehydrogenase (quinone) activity oxidoreductase activity, acting on NAD(P)H catalytic activity oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor NADH dehydrogenase (quinone) (non-electrogenic) activity NADH dehydrogenase activity binding quinone binding small molecule binding	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	cell periphery cellular anatomical structure plasma membrane membrane protein-containing complex catalytic complex membrane protein complex oxidoreductase complex NADH dehydrogenase complex
C [auth N], I [auth D]	NADH-QUINONE OXIDOREDUCTASE SUBUNIT N	-	-	-
B [auth M], H [auth C]	NADH-QUINONE OXIDOREDUCTASE SUBUNIT M	-	-	-
A [auth L], G [auth B]	NADH-QUINONE OXIDOREDUCTASE SUBUNIT L	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
D [auth K], J [auth G]	IPR001133	NADH-ubiquinone oxidoreductase chain 4L/K	Family
D [auth K], J [auth G]	IPR039428	NADH-ubiquinone oxidoreductase chain 4L/Mnh complex subunit C1-like	Family

Membrane Protein Annotation: OPM OPM Database Homepage

Chains	External Link	Type	Class	Superfamily	Family
D [auth K], J [auth G]	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
D [auth K], J [auth G]	PDBTM	Annotated as membrane protein by PDBTM

Membrane Protein Annotation: MemProtMD MemProtMD Database Homepage

Chains	External Link	Comment
D [auth K], J [auth G]	MemProtMD	Annotated as membrane protein by MemProtMD

Membrane Protein Annotation: mpstruc mpstruc Database Homepage

Chains	Resource Link	Group	Subgroup	Protein
D [auth K], J [auth G]	mpstruc	TRANSMEMBRANE PROTEINS: ALPHA-HELICAL	Electron Transport Chain Complexes: Complex I	Complex I membrane domain

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.

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