9BRR | pdb_00009brr

Intact V-ATPase State 3 in synaptophysin knock-out isolated synaptic vesicles

External Resource: Annotation

Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Membrane Protein Annotation: mpstruc

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
Y [auth 6]	WD40	e9brr61	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: WD40	ECOD (v294.2)
X	WD40	e9brrX1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: WD40	ECOD (v294.2)
W [auth V]	WD40	e9brrV1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: WD40	ECOD (v294.2)
V [auth T]	WD40	e9brrT1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: WD40	ECOD (v294.2)
U [auth R]	WD40	e9brrR1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: WD40	ECOD (v294.2)
T [auth Q]	WD40	e9brrQ1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: WD40	ECOD (v294.2)
S [auth 9]	WD40	e9brr91	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: WD40	ECOD (v294.2)
R [auth 8]	WD40	e9brr81	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: WD40	ECOD (v294.2)
Q [auth 7]	WD40	e9brr71	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: WD40	ECOD (v294.2)
P [auth 5]	WD40	e9brr51	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: WD40	ECOD (v294.2)
O [auth 4]	WD40	e9brr41	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: WD40	ECOD (v294.2)
N [auth 3]	WD40	e9brr31	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: WD40	ECOD (v294.2)
M [auth 2]	WD40	e9brr21	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: WD40	ECOD (v294.2)
L [auth 0]	WD40	e9brr01	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: WD40	ECOD (v294.2)
K [auth 1]	WD40	e9brr11	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: WD40	ECOD (v294.2)
J [auth o]	WD40	e9brro1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: WD40	ECOD (v294.2)
I [auth n]	WD40	e9brrn1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: WD40	ECOD (v294.2)
H [auth m]	WD40	e9brrm1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: WD40	ECOD (v294.2)
G [auth l]	WD40	e9brrl1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: WD40	ECOD (v294.2)
F [auth k]	WD40	e9brrk1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: WD40	ECOD (v294.2)
E [auth j]	WD40	e9brrj1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: WD40	ECOD (v294.2)
D [auth i]	WD40	e9brri1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: WD40	ECOD (v294.2)
C [auth h]	WD40	e9brrh1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: WD40	ECOD (v294.2)
B [auth g]	WD40	e9brrg1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: WD40	ECOD (v294.2)
AA [auth d]	WD40	e9brrd1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: WD40	ECOD (v294.2)
Z [auth U]	WD40	e9brrU1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: WD40	ECOD (v294.2)
A [auth b]	WD40	e9brrb1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: WD40	ECOD (v294.2)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
Y [auth 6]	PF03223	V-ATPase subunit C (V-ATPase_C)	V-ATPase subunit C	-	Family
X	PF01990	ATP synthase (F/14-kDa) subunit (ATP-synt_F)	ATP synthase (F/14-kDa) subunit	-	Family
U [auth R], V [auth T], W [auth V]	PF03179	Vacuolar (H+)-ATPase G subunit (V-ATPase_G)	Vacuolar (H+)-ATPase G subunit	-	Coiled-coil
R [auth 8], S [auth 9], T [auth Q]	PF01991	ATP synthase (E/31 kDa) subunit (vATP-synt_E)	ATP synthase (E/31 kDa) subunit	-	Family
Q [auth 7]	PF01813	ATP synthase subunit D (ATP-synt_D)	ATP synthase subunit D	-	Family
N [auth 3], O [auth 4], P [auth 5]	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
N [auth 3], O [auth 4], P [auth 5]	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
N [auth 3], O [auth 4], P [auth 5]	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
K [auth 1], L [auth 0], M [auth 2]	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
K [auth 1], L [auth 0], M [auth 2]	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
K [auth 1], L [auth 0], M [auth 2]	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
K [auth 1], L [auth 0], M [auth 2]	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
Z [auth U]	PF11698	V-ATPase subunit H (V-ATPase_H_C)	V-ATPase subunit H	-	Repeat
Z [auth U]	PF03224	V-ATPase subunit H (V-ATPase_H_N)	V-ATPase subunit H	-	Repeat

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
Y [auth 6]	IPR004907	ATPase, V1 complex, subunit C	Family
Y [auth 6]	IPR036132	Vacuolar ATP synthase subunit C superfamily	Homologous Superfamily
X	IPR036906	ATPase, V1 complex, subunit F superfamily	Homologous Superfamily
X	IPR005772	ATPase, V1 complex, subunit F, eukaryotic	Family
X	IPR008218	ATPase, V1 complex, subunit F	Family
U [auth R], V [auth T], W [auth V]	IPR005124	Vacuolar (H+)-ATPase G subunit	Family
R [auth 8], S [auth 9], T [auth Q]	IPR038495	V-type ATPase subunit E, C-terminal domain superfamily	Homologous Superfamily
R [auth 8], S [auth 9], T [auth Q]	IPR002842	V-type ATPase subunit E	Family
Q [auth 7]	IPR002699	ATPase, V1 complex, subunit D	Family
N [auth 3], O [auth 4], P [auth 5]	IPR004100	ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain	Domain
N [auth 3], O [auth 4], P [auth 5]	IPR005723	ATPase, V1 complex, subunit B	Family
N [auth 3], O [auth 4], P [auth 5]	IPR022879	V-type ATP synthase regulatory subunit B/beta	Family
N [auth 3], O [auth 4], P [auth 5]	IPR020003	ATPase, alpha/beta subunit, nucleotide-binding domain, active site	Active Site
N [auth 3], O [auth 4], P [auth 5]	IPR000194	ATPase, F1/V1/A1 complex, alpha/beta subunit, nucleotide-binding domain	Domain
N [auth 3], O [auth 4], P [auth 5]	IPR055190	ATP synthase A/B type, C-terminal domain	Domain
N [auth 3], O [auth 4], P [auth 5]	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
K [auth 1], L [auth 0], M [auth 2]	IPR022878	V-type ATP synthase catalytic alpha chain	Family
K [auth 1], L [auth 0], M [auth 2]	IPR024034	ATPase, F1/V1 complex, beta/alpha subunit, C-terminal	Homologous Superfamily
K [auth 1], L [auth 0], M [auth 2]	IPR036121	ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain superfamily	Homologous Superfamily
K [auth 1], L [auth 0], M [auth 2]	IPR031686	ATPsynthase alpha/beta subunit, barrel-sandwich domain	Domain
K [auth 1], L [auth 0], M [auth 2]	IPR000194	ATPase, F1/V1/A1 complex, alpha/beta subunit, nucleotide-binding domain	Domain
K [auth 1], L [auth 0], M [auth 2]	IPR005725	ATPase, V1 complex, subunit A	Family
K [auth 1], L [auth 0], M [auth 2]	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
K [auth 1], L [auth 0], M [auth 2]	IPR004100	ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain	Domain
K [auth 1], L [auth 0], M [auth 2]	IPR023366	ATP synthase subunit alpha, N-terminal domain-like superfamily	Homologous Superfamily
K [auth 1], L [auth 0], M [auth 2]	IPR020003	ATPase, alpha/beta subunit, nucleotide-binding domain, active site	Active Site
K [auth 1], L [auth 0], M [auth 2]	IPR055190	ATP synthase A/B type, C-terminal domain	Domain
B [auth g], C [auth h], D [auth i], E [auth j], F [auth k], B [auth g], C [auth h], D [auth i], E [auth j], F [auth k], G [auth l], H [auth m], I [auth n], J [auth o]	IPR035921	F/V-ATP synthase subunit C superfamily	Homologous Superfamily
B [auth g], C [auth h], D [auth i], E [auth j], F [auth k], B [auth g], C [auth h], D [auth i], E [auth j], F [auth k], G [auth l], H [auth m], I [auth n], J [auth o]	IPR002379	V-ATPase proteolipid subunit C-like domain	Domain
B [auth g], C [auth h], D [auth i], E [auth j], F [auth k], B [auth g], C [auth h], D [auth i], E [auth j], F [auth k], G [auth l], H [auth m], I [auth n], J [auth o]	IPR011555	V-ATPase proteolipid subunit C, eukaryotic	Family
B [auth g], C [auth h], D [auth i], E [auth j], F [auth k], B [auth g], C [auth h], D [auth i], E [auth j], F [auth k], G [auth l], H [auth m], I [auth n], J [auth o]	IPR000245	V-ATPase proteolipid subunit	Family
FA [auth p]	IPR056780	Renin receptor-like, C-terminal transmembrane spanning segment	Domain
FA [auth p]	IPR012493	Renin receptor-like	Family
FA [auth p]	IPR057318	Renin receptor, N-terminal domain	Domain
EA [auth c]	IPR046755	V-type proton ATPase subunit S1, luminal domain	Domain
EA [auth c]	IPR008388	V0 complex accessory subunit Ac45	Family
EA [auth c]	IPR046756	V-type proton ATPase subunit S1/VOA1, transmembrane domain	Domain
DA [auth f]	IPR056552	Ribonucl_Kappa	Unknown
DA [auth f]	IPR026770	Ribonuclease kappa	Family
CA [auth e]	IPR017385	ATPase, V0 complex, subunit e1/e2, metazoa	Family
CA [auth e]	IPR008389	ATPase, V0 complex, subunit e1/e2	Family
BA [auth a]	IPR026028	ATPase, V0 complex, subunit 116kDa, eukaryotic	Family
BA [auth a]	IPR002490	V-type ATPase, V0 complex, 116kDa subunit family	Family
AA [auth d]	IPR044911	V-type ATP synthase C/D subunit, domain 3 superfamily	Homologous Superfamily
AA [auth d]	IPR036079	V-type ATP synthase subunit C/D subunit superfamily	Homologous Superfamily
AA [auth d]	IPR035067	V-type ATPase subunit C/D	Homologous Superfamily
AA [auth d]	IPR002843	ATPase, V0 complex, C/D subunit	Family
AA [auth d]	IPR016727	ATPase, V0 complex, subunit D	Family
Z [auth U]	IPR004908	ATPase, V1 complex, subunit H	Family
Z [auth U]	IPR016024	Armadillo-type fold	Homologous Superfamily
Z [auth U]	IPR011989	Armadillo-like helical	Homologous Superfamily
Z [auth U]	IPR038497	ATPase, V1 complex, subunit H, C-terminal domain superfamily	Homologous Superfamily
Z [auth U]	IPR011987	ATPase, V1 complex, subunit H, C-terminal	Domain
A [auth b]	IPR035921	F/V-ATP synthase subunit C superfamily	Homologous Superfamily
A [auth b]	IPR002379	V-ATPase proteolipid subunit C-like domain	Domain
A [auth b]	IPR000245	V-ATPase proteolipid subunit	Family

Membrane Protein Annotation: mpstruc mpstruc Database Homepage

Chains	Resource Link	Group	Subgroup	Protein
A [auth b], AA [auth d], B [auth g], BA [auth a], C [auth h] A [auth b], AA [auth d], B [auth g], BA [auth a], C [auth h], CA [auth e], D [auth i], DA [auth f], E [auth j], EA [auth c], F [auth k], FA [auth p], G [auth l], H [auth m], I [auth n], J [auth o], K [auth 1], L [auth 0], M [auth 2], N [auth 3], O [auth 4], P [auth 5], Q [auth 7], R [auth 8], S [auth 9], T [auth Q], U [auth R], V [auth T], W [auth V], X, Y [auth 6], Z [auth U]	mpstruc	TRANSMEMBRANE PROTEINS: ALPHA-HELICAL	Vacuolar ATPase (V-ATPase)	V-ATPase, state 1 with synaptophysin in brain isolated synaptic vesicles

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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.