7KHR | pdb_00007khr

Cryo-EM structure of bafilomycin A1-bound intact V-ATPase from bovine brain

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)
G	SCOP2B Superfamily	Vacuolar ATP synthase subunit C	8098568	3001744	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)
P	DctP	e7khrP1	A: alpha bundles	X: CNF1/YfiH-like putative cysteine hydrolases	H: Bromodomain	T: Bromodomain	F: DctP	ECOD (develop294)
M	DctP	e7khrM1	A: alpha bundles	X: CNF1/YfiH-like putative cysteine hydrolases	H: Bromodomain	T: Bromodomain	F: DctP	ECOD (develop294)
N	Omp85	e7khrN1	A: alpha bundles	X: CNF1/YfiH-like putative cysteine hydrolases	H: Bromodomain	T: Bromodomain	F: Omp85	ECOD (develop294)
O	Omp85	e7khrO1	A: alpha bundles	X: CNF1/YfiH-like putative cysteine hydrolases	H: Bromodomain	T: Bromodomain	F: Omp85	ECOD (develop294)
L	DctP	e7khrL1	A: alpha bundles	X: CNF1/YfiH-like putative cysteine hydrolases	H: Bromodomain	T: Bromodomain	F: DctP	ECOD (develop294)
I	Omp85	e7khrI1	A: alpha bundles	X: CNF1/YfiH-like putative cysteine hydrolases	H: Bromodomain	T: Bromodomain	F: Omp85	ECOD (develop294)
J	Omp85	e7khrJ1	A: alpha bundles	X: CNF1/YfiH-like putative cysteine hydrolases	H: Bromodomain	T: Bromodomain	F: Omp85	ECOD (develop294)
K	DctP	e7khrK1	A: alpha bundles	X: CNF1/YfiH-like putative cysteine hydrolases	H: Bromodomain	T: Bromodomain	F: DctP	ECOD (develop294)
H	DctP	e7khrH1	A: alpha bundles	X: CNF1/YfiH-like putative cysteine hydrolases	H: Bromodomain	T: Bromodomain	F: DctP	ECOD (develop294)
G	DctP	e7khrG1	A: alpha bundles	X: CNF1/YfiH-like putative cysteine hydrolases	H: Bromodomain	T: Bromodomain	F: DctP	ECOD (develop294)
D	DctP	e7khrD1	A: alpha bundles	X: CNF1/YfiH-like putative cysteine hydrolases	H: Bromodomain	T: Bromodomain	F: DctP	ECOD (develop294)
E	Omp85	e7khrE1	A: alpha bundles	X: CNF1/YfiH-like putative cysteine hydrolases	H: Bromodomain	T: Bromodomain	F: Omp85	ECOD (develop294)
F	Omp85	e7khrF1	A: alpha bundles	X: CNF1/YfiH-like putative cysteine hydrolases	H: Bromodomain	T: Bromodomain	F: Omp85	ECOD (develop294)
AA [auth m]	Omp85	e7khrm1	A: alpha bundles	X: CNF1/YfiH-like putative cysteine hydrolases	H: Bromodomain	T: Bromodomain	F: Omp85	ECOD (develop294)
BA [auth n]	Omp85	e7khrn1	A: alpha bundles	X: CNF1/YfiH-like putative cysteine hydrolases	H: Bromodomain	T: Bromodomain	F: Omp85	ECOD (develop294)
EA [auth q]	Omp85	e7khrq1	A: alpha bundles	X: CNF1/YfiH-like putative cysteine hydrolases	H: Bromodomain	T: Bromodomain	F: Omp85	ECOD (develop294)
W [auth c]	Omp85	e7khrc1	A: alpha bundles	X: CNF1/YfiH-like putative cysteine hydrolases	H: Bromodomain	T: Bromodomain	F: Omp85	ECOD (develop294)
Y [auth k]	Omp85	e7khrk1	A: alpha bundles	X: CNF1/YfiH-like putative cysteine hydrolases	H: Bromodomain	T: Bromodomain	F: Omp85	ECOD (develop294)
Z [auth l]	Omp85	e7khrl1	A: alpha bundles	X: CNF1/YfiH-like putative cysteine hydrolases	H: Bromodomain	T: Bromodomain	F: Omp85	ECOD (develop294)
X [auth g]	Omp85	e7khrg1	A: alpha bundles	X: CNF1/YfiH-like putative cysteine hydrolases	H: Bromodomain	T: Bromodomain	F: Omp85	ECOD (develop294)
DA [auth p]	Omp85	e7khrp1	A: alpha bundles	X: CNF1/YfiH-like putative cysteine hydrolases	H: Bromodomain	T: Bromodomain	F: Omp85	ECOD (develop294)
CA [auth o]	DctP	e7khro1	A: alpha bundles	X: CNF1/YfiH-like putative cysteine hydrolases	H: Bromodomain	T: Bromodomain	F: DctP	ECOD (develop294)
S [auth d]	DctP	e7khrd1	A: alpha bundles	X: CNF1/YfiH-like putative cysteine hydrolases	H: Bromodomain	T: Bromodomain	F: DctP	ECOD (develop294)
A	Omp85	e7khrA1	A: alpha bundles	X: CNF1/YfiH-like putative cysteine hydrolases	H: Bromodomain	T: Bromodomain	F: Omp85	ECOD (develop294)
B	Omp85	e7khrB1	A: alpha bundles	X: CNF1/YfiH-like putative cysteine hydrolases	H: Bromodomain	T: Bromodomain	F: Omp85	ECOD (develop294)
C	DctP	e7khrC1	A: alpha bundles	X: CNF1/YfiH-like putative cysteine hydrolases	H: Bromodomain	T: Bromodomain	F: DctP	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
I	3.30.2320.30	Alpha Beta	2-Layer Sandwich	hypothetical protein PF0899 fold	ATP synthase, E subunit, C-terminal	CATH (utative)
J	3.30.2320.30	Alpha Beta	2-Layer Sandwich	hypothetical protein PF0899 fold	ATP synthase, E subunit, C-terminal	CATH (utative)
K	3.30.2320.30	Alpha Beta	2-Layer Sandwich	hypothetical protein PF0899 fold	ATP synthase, E subunit, C-terminal	CATH (utative)
H	1.10.287.3240	Mainly Alpha	Orthogonal Bundle	Helix Hairpins		CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
P	PF11698	V-ATPase subunit H (V-ATPase_H_C)	V-ATPase subunit H	-	Repeat
P	PF00137	ATP synthase subunit C (ATP-synt_C)	ATP synthase subunit C	This domain is found in the subunit c of ATP synthases and similar sequences from all cellular organisms. It forms two alpha-helices [1-4].	Domain
M, N, O	PF00137	ATP synthase subunit C (ATP-synt_C)	ATP synthase subunit C	This domain is found in the subunit c of ATP synthases and similar sequences from all cellular organisms. It forms two alpha-helices [1-4].	Domain
L	PF01990	ATP synthase (F/14-kDa) subunit (ATP-synt_F)	ATP synthase (F/14-kDa) subunit	-	Family
L	PF00137	ATP synthase subunit C (ATP-synt_C)	ATP synthase subunit C	This domain is found in the subunit c of ATP synthases and similar sequences from all cellular organisms. It forms two alpha-helices [1-4].	Domain
I, J, K	PF01991	ATP synthase (E/31 kDa) subunit (vATP-synt_E)	ATP synthase (E/31 kDa) subunit	-	Family
I, J, K	PF00137	ATP synthase subunit C (ATP-synt_C)	ATP synthase subunit C	This domain is found in the subunit c of ATP synthases and similar sequences from all cellular organisms. It forms two alpha-helices [1-4].	Domain
H	PF01813	ATP synthase subunit D (ATP-synt_D)	ATP synthase subunit D	-	Family
G	PF03223	V-ATPase subunit C (V-ATPase_C)	V-ATPase subunit C	-	Family
G	PF00137	ATP synthase subunit C (ATP-synt_C)	ATP synthase subunit C	This domain is found in the subunit c of ATP synthases and similar sequences from all cellular organisms. It forms two alpha-helices [1-4].	Domain
D, E, F	PF00006	ATP synthase alpha/beta family, nucleotide-binding domain (ATP-synt_ab)	ATP synthase alpha/beta family, nucleotide-binding domain	This entry includes the ATP synthase alpha and beta subunits, the ATP synthase associated with flagella and the termination factor Rho.	Domain
D, E, F	PF05493	ATP synthase subunit H (ATP_synt_H)	ATP synthase subunit H	-	Family
D, E, F	PF22919	C-terminal domain of V and A type ATP synthase (ATP-synt_VA_C)	C-terminal domain of V and A type ATP synthase	This entry represents a small alpha helical domain found at the C-terminus of a variety of ATP synthases.	Domain
D, E, F	PF01992	ATP synthase (C/AC39) subunit (vATP-synt_AC39)	ATP synthase (C/AC39) subunit	-	Family
D, E, F	PF02874	ATP synthase alpha/beta family, beta-barrel domain (ATP-synt_ab_N)	ATP synthase alpha/beta family, beta-barrel domain	This family includes the ATP synthase alpha and beta subunits the ATP synthase associated with flagella.	Domain
A, B, C	PF00006	ATP synthase alpha/beta family, nucleotide-binding domain (ATP-synt_ab)	ATP synthase alpha/beta family, nucleotide-binding domain	This entry includes the ATP synthase alpha and beta subunits, the ATP synthase associated with flagella and the termination factor Rho.	Domain
A, B, C	PF22919	C-terminal domain of V and A type ATP synthase (ATP-synt_VA_C)	C-terminal domain of V and A type ATP synthase	This entry represents a small alpha helical domain found at the C-terminus of a variety of ATP synthases.	Domain
A, B, C	PF16886	ATPsynthase alpha/beta subunit barrel-sandwich domain (ATP-synt_ab_Xtn)	ATPsynthase alpha/beta subunit barrel-sandwich domain	This barrel-sandwich domain is found in the alpha-beta catalytic subunit of VATA or V-type proton ATPase catalytic subunit at the N-terminal end. This domain has a circularly permuted topology compared to other barrel-sandwich domains. In VATA barrel ...	This barrel-sandwich domain is found in the alpha-beta catalytic subunit of VATA or V-type proton ATPase catalytic subunit at the N-terminal end. This domain has a circularly permuted topology compared to other barrel-sandwich domains. In VATA barrel-sandwich domain the C-terminal strand is circularly permuted and occupies the spatial position of the N-terminal strand in other hybrid domains.	Domain
A, B, C	PF01496	V-type ATPase 116kDa subunit family (V_ATPase_I)	V-type ATPase 116kDa subunit family	-	Family
A, B, C	PF02874	ATP synthase alpha/beta family, beta-barrel domain (ATP-synt_ab_N)	ATP synthase alpha/beta family, beta-barrel domain	This family includes the ATP synthase alpha and beta subunits the ATP synthase associated with flagella.	Domain
A, B, C	PF00137	ATP synthase subunit C (ATP-synt_C)	ATP synthase subunit C	This domain is found in the subunit c of ATP synthases and similar sequences from all cellular organisms. It forms two alpha-helices [1-4].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
Q [auth a]	IPR026028	ATPase, V0 complex, subunit 116kDa, eukaryotic	Family
Q [auth a]	IPR002490	V-type ATPase, V0 complex, 116kDa subunit family	Family
P	IPR011989	Armadillo-like helical	Homologous Superfamily
P	IPR004908	ATPase, V1 complex, subunit H	Family
P	IPR016024	Armadillo-type fold	Homologous Superfamily
P	IPR038497	ATPase, V1 complex, subunit H, C-terminal domain superfamily	Homologous Superfamily
P	IPR011987	ATPase, V1 complex, subunit H, C-terminal	Domain
M, N, O	IPR005124	Vacuolar (H+)-ATPase G subunit	Family
L	IPR005772	ATPase, V1 complex, subunit F, eukaryotic	Family
L	IPR036906	ATPase, V1 complex, subunit F superfamily	Homologous Superfamily
L	IPR008218	ATPase, V1 complex, subunit F	Family
I, J, K	IPR002842	V-type ATPase subunit E	Family
I, J, K	IPR038495	V-type ATPase subunit E, C-terminal domain superfamily	Homologous Superfamily
H	IPR002699	ATPase, V1 complex, subunit D	Family
G	IPR004907	ATPase, V1 complex, subunit C	Family
G	IPR036132	Vacuolar ATP synthase subunit C superfamily	Homologous Superfamily
D, E, F	IPR004100	ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain	Domain
D, E, F	IPR005723	ATPase, V1 complex, subunit B	Family
D, E, F	IPR022879	V-type ATP synthase regulatory subunit B/beta	Family
D, E, F	IPR020003	ATPase, alpha/beta subunit, nucleotide-binding domain, active site	Active Site
D, E, F	IPR000194	ATPase, F1/V1/A1 complex, alpha/beta subunit, nucleotide-binding domain	Domain
D, E, F	IPR055190	ATP synthase A/B type, C-terminal domain	Domain
D, E, F	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
FA [auth f]	IPR056552	Ribonucl_Kappa	Unknown
FA [auth f]	IPR026770	Ribonuclease kappa	Family
AA [auth m], BA [auth n], CA [auth o], DA [auth p], EA [auth q], AA [auth m], BA [auth n], CA [auth o], DA [auth p], EA [auth q], W [auth c], X [auth g], Y [auth k], Z [auth l]	IPR035921	F/V-ATP synthase subunit C superfamily	Homologous Superfamily
AA [auth m], BA [auth n], CA [auth o], DA [auth p], EA [auth q], AA [auth m], BA [auth n], CA [auth o], DA [auth p], EA [auth q], W [auth c], X [auth g], Y [auth k], Z [auth l]	IPR000245	V-ATPase proteolipid subunit	Family
AA [auth m], BA [auth n], CA [auth o], DA [auth p], EA [auth q], AA [auth m], BA [auth n], CA [auth o], DA [auth p], EA [auth q], W [auth c], X [auth g], Y [auth k], Z [auth l]	IPR002379	V-ATPase proteolipid subunit C-like domain	Domain
AA [auth m], BA [auth n], CA [auth o], DA [auth p], EA [auth q], AA [auth m], BA [auth n], CA [auth o], DA [auth p], EA [auth q], W [auth c], X [auth g], Y [auth k], Z [auth l]	IPR011555	V-ATPase proteolipid subunit C, eukaryotic	Family
V [auth r]	IPR056780	Renin receptor-like, C-terminal transmembrane spanning segment	Domain
V [auth r]	IPR012493	Renin receptor-like	Family
V [auth r]	IPR057318	Renin receptor, N-terminal domain	Domain
U [auth s]	IPR046755	V-type proton ATPase subunit S1, luminal domain	Domain
U [auth s]	IPR008388	V0 complex accessory subunit Ac45	Family
U [auth s]	IPR046756	V-type proton ATPase subunit S1/VOA1, transmembrane domain	Domain
T [auth e]	IPR017385	ATPase, V0 complex, subunit e1/e2, metazoa	Family
T [auth e]	IPR008389	ATPase, V0 complex, subunit e1/e2	Family
S [auth d]	IPR044911	V-type ATP synthase C/D subunit, domain 3 superfamily	Homologous Superfamily
S [auth d]	IPR002843	ATPase, V0 complex, C/D subunit	Family
S [auth d]	IPR036079	V-type ATP synthase subunit C/D subunit superfamily	Homologous Superfamily
S [auth d]	IPR035067	V-type ATPase subunit C/D	Homologous Superfamily
S [auth d]	IPR016727	ATPase, V0 complex, subunit D	Family
R [auth b]	IPR035921	F/V-ATP synthase subunit C superfamily	Homologous Superfamily
R [auth b]	IPR000245	V-ATPase proteolipid subunit	Family
R [auth b]	IPR002379	V-ATPase proteolipid subunit C-like domain	Domain
A, B, C	IPR022878	V-type ATP synthase catalytic alpha chain	Family
A, B, C	IPR024034	ATPase, F1/V1 complex, beta/alpha subunit, C-terminal	Homologous Superfamily
A, B, C	IPR036121	ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain superfamily	Homologous Superfamily
A, B, C	IPR031686	ATPsynthase alpha/beta subunit, barrel-sandwich domain	Domain
A, B, C	IPR000194	ATPase, F1/V1/A1 complex, alpha/beta subunit, nucleotide-binding domain	Domain
A, B, C	IPR005725	ATPase, V1 complex, subunit A	Family
A, B, C	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
A, B, C	IPR004100	ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain	Domain
A, B, C	IPR023366	ATP synthase subunit alpha, N-terminal domain-like superfamily	Homologous Superfamily
A, B, C	IPR020003	ATPase, alpha/beta subunit, nucleotide-binding domain, active site	Active Site
A, B, C	IPR055190	ATP synthase A/B type, C-terminal domain	Domain

Membrane Protein Annotation: OPM OPM Database Homepage

Chains	External Link	Type	Class	Superfamily	Family
A, AA [auth m], B, BA [auth n], C A, AA [auth m], B, BA [auth n], C, CA [auth o], D, DA [auth p], E, EA [auth q], F, FA [auth f], G, H, I, J, K, L, M, N, O, P, Q [auth a], R [auth b], S [auth d], T [auth e], U [auth s], V [auth r], W [auth c], X [auth g], Y [auth k], Z [auth l]	OPM	Transmembrane	Alpha-helical polytopic	Proton or Sodium translocating F-type, V-type and A-type ATPases	V-type and F-type ATPases

Membrane Protein Annotation: PDBTM PDBTM Database Homepage

Chains	External Link	Comment
A, AA [auth m], B, BA [auth n], C A, AA [auth m], B, BA [auth n], C, CA [auth o], D, DA [auth p], E, EA [auth q], F, FA [auth f], G, H, I, J, K, L, M, N, O, P, Q [auth a], R [auth b], S [auth d], T [auth e], U [auth s], V [auth r], W [auth c], X [auth g], Y [auth k], Z [auth l]	PDBTM	Annotated as membrane protein by PDBTM

Membrane Protein Annotation: mpstruc mpstruc Database Homepage

Chains	Resource Link	Group	Subgroup	Protein
A, AA [auth m], B, BA [auth n], C A, AA [auth m], B, BA [auth n], C, CA [auth o], D, DA [auth p], E, EA [auth q], F, FA [auth f], G, H, I, J, K, L, M, N, O, P, Q [auth a], R [auth b], S [auth d], T [auth e], U [auth s], V [auth r], W [auth c], X [auth g], Y [auth k], Z [auth l]	mpstruc	TRANSMEMBRANE PROTEINS: ALPHA-HELICAL	Vacuolar ATPase (V-ATPase)	V-ATPase with bound bafilomycin A1