9BRQ | pdb_00009brq

Intact V-ATPase State 3 and synaptophysin complex in mouse brain 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)
X [auth 6]	WD40	e9brq61	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: WD40	ECOD (v294.2)
W [auth X]	WD40	e9brqX1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: WD40	ECOD (v294.2)
V	WD40	e9brqV1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: WD40	ECOD (v294.2)
U [auth T]	WD40	e9brqT1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: WD40	ECOD (v294.2)
T [auth R]	WD40	e9brqR1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: WD40	ECOD (v294.2)
S [auth Q]	WD40	e9brqQ1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: WD40	ECOD (v294.2)
R [auth 9]	WD40	e9brq91	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: WD40	ECOD (v294.2)
Q [auth 8]	WD40	e9brq81	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: WD40	ECOD (v294.2)
P [auth 7]	WD40	e9brq71	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: WD40	ECOD (v294.2)
O [auth 5]	WD40	e9brq51	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: WD40	ECOD (v294.2)
N [auth 4]	WD40	e9brq41	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: WD40	ECOD (v294.2)
M [auth 3]	WD40	e9brq31	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: WD40	ECOD (v294.2)
L [auth 2]	WD40	e9brq21	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: WD40	ECOD (v294.2)
K [auth 1]	WD40	e9brq11	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: WD40	ECOD (v294.2)
DA [auth 0]	WD40	e9brq01	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: WD40	ECOD (v294.2)
J [auth o]	WD40	e9brqo1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: WD40	ECOD (v294.2)
I [auth n]	WD40	e9brqn1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: WD40	ECOD (v294.2)
H [auth m]	WD40	e9brqm1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: WD40	ECOD (v294.2)
G [auth l]	WD40	e9brql1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: WD40	ECOD (v294.2)
F [auth k]	WD40	e9brqk1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: WD40	ECOD (v294.2)
E [auth j]	WD40	e9brqj1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: WD40	ECOD (v294.2)
D [auth i]	WD40	e9brqi1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: WD40	ECOD (v294.2)
C [auth h]	WD40	e9brqh1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: WD40	ECOD (v294.2)
B [auth g]	WD40	e9brqg1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: WD40	ECOD (v294.2)
Z [auth d]	WD40	e9brqd1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: WD40	ECOD (v294.2)
Y [auth U]	WD40	e9brqU1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: WD40	ECOD (v294.2)
A [auth b]	WD40	e9brqb1	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
X [auth 6]	PF03223	V-ATPase subunit C (V-ATPase_C)	V-ATPase subunit C	-	Family
W [auth X]	PF01990	ATP synthase (F/14-kDa) subunit (ATP-synt_F)	ATP synthase (F/14-kDa) subunit	-	Family
T [auth R], U [auth T], V	PF03179	Vacuolar (H+)-ATPase G subunit (V-ATPase_G)	Vacuolar (H+)-ATPase G subunit	-	Coiled-coil
Q [auth 8], R [auth 9], S [auth Q]	PF01991	ATP synthase (E/31 kDa) subunit (vATP-synt_E)	ATP synthase (E/31 kDa) subunit	-	Family
P [auth 7]	PF01813	ATP synthase subunit D (ATP-synt_D)	ATP synthase subunit D	-	Family
M [auth 3], N [auth 4], O [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
M [auth 3], N [auth 4], O [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
M [auth 3], N [auth 4], O [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
DA [auth 0], K [auth 1], L [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
DA [auth 0], K [auth 1], L [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
DA [auth 0], K [auth 1], L [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
DA [auth 0], K [auth 1], L [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
Y [auth U]	PF11698	V-ATPase subunit H (V-ATPase_H_C)	V-ATPase subunit H	-	Repeat
Y [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
X [auth 6]	IPR004907	ATPase, V1 complex, subunit C	Family
X [auth 6]	IPR036132	Vacuolar ATP synthase subunit C superfamily	Homologous Superfamily
W [auth X]	IPR005772	ATPase, V1 complex, subunit F, eukaryotic	Family
W [auth X]	IPR036906	ATPase, V1 complex, subunit F superfamily	Homologous Superfamily
W [auth X]	IPR008218	ATPase, V1 complex, subunit F	Family
T [auth R], U [auth T], V	IPR005124	Vacuolar (H+)-ATPase G subunit	Family
Q [auth 8], R [auth 9], S [auth Q]	IPR038495	V-type ATPase subunit E, C-terminal domain superfamily	Homologous Superfamily
Q [auth 8], R [auth 9], S [auth Q]	IPR002842	V-type ATPase subunit E	Family
P [auth 7]	IPR002699	ATPase, V1 complex, subunit D	Family
M [auth 3], N [auth 4], O [auth 5]	IPR004100	ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain	Domain
M [auth 3], N [auth 4], O [auth 5]	IPR005723	ATPase, V1 complex, subunit B	Family
M [auth 3], N [auth 4], O [auth 5]	IPR022879	V-type ATP synthase regulatory subunit B/beta	Family
M [auth 3], N [auth 4], O [auth 5]	IPR020003	ATPase, alpha/beta subunit, nucleotide-binding domain, active site	Active Site
M [auth 3], N [auth 4], O [auth 5]	IPR000194	ATPase, F1/V1/A1 complex, alpha/beta subunit, nucleotide-binding domain	Domain
M [auth 3], N [auth 4], O [auth 5]	IPR055190	ATP synthase A/B type, C-terminal domain	Domain
M [auth 3], N [auth 4], O [auth 5]	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
DA [auth 0], K [auth 1], L [auth 2]	IPR022878	V-type ATP synthase catalytic alpha chain	Family
DA [auth 0], K [auth 1], L [auth 2]	IPR024034	ATPase, F1/V1 complex, beta/alpha subunit, C-terminal	Homologous Superfamily
DA [auth 0], K [auth 1], L [auth 2]	IPR036121	ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain superfamily	Homologous Superfamily
DA [auth 0], K [auth 1], L [auth 2]	IPR031686	ATPsynthase alpha/beta subunit, barrel-sandwich domain	Domain
DA [auth 0], K [auth 1], L [auth 2]	IPR000194	ATPase, F1/V1/A1 complex, alpha/beta subunit, nucleotide-binding domain	Domain
DA [auth 0], K [auth 1], L [auth 2]	IPR005725	ATPase, V1 complex, subunit A	Family
DA [auth 0], K [auth 1], L [auth 2]	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
DA [auth 0], K [auth 1], L [auth 2]	IPR004100	ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain	Domain
DA [auth 0], K [auth 1], L [auth 2]	IPR023366	ATP synthase subunit alpha, N-terminal domain-like superfamily	Homologous Superfamily
DA [auth 0], K [auth 1], L [auth 2]	IPR020003	ATPase, alpha/beta subunit, nucleotide-binding domain, active site	Active Site
DA [auth 0], K [auth 1], L [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
GA [auth e]	IPR017385	ATPase, V0 complex, subunit e1/e2, metazoa	Family
GA [auth e]	IPR008389	ATPase, V0 complex, subunit e1/e2	Family
FA [auth s]	IPR001285	Synaptophysin/synaptoporin	Family
FA [auth s]	IPR008253	Marvel domain	Domain
EA [auth f]	IPR056552	Ribonucl_Kappa	Unknown
EA [auth f]	IPR026770	Ribonuclease kappa	Family
CA [auth p]	IPR056780	Renin receptor-like, C-terminal transmembrane spanning segment	Domain
CA [auth p]	IPR012493	Renin receptor-like	Family
CA [auth p]	IPR057318	Renin receptor, N-terminal domain	Domain
BA [auth c]	IPR046755	V-type proton ATPase subunit S1, luminal domain	Domain
BA [auth c]	IPR008388	V0 complex accessory subunit Ac45	Family
BA [auth c]	IPR046756	V-type proton ATPase subunit S1/VOA1, transmembrane domain	Domain
AA [auth a]	IPR026028	ATPase, V0 complex, subunit 116kDa, eukaryotic	Family
AA [auth a]	IPR002490	V-type ATPase, V0 complex, 116kDa subunit family	Family
Z [auth d]	IPR044911	V-type ATP synthase C/D subunit, domain 3 superfamily	Homologous Superfamily
Z [auth d]	IPR036079	V-type ATP synthase subunit C/D subunit superfamily	Homologous Superfamily
Z [auth d]	IPR035067	V-type ATPase subunit C/D	Homologous Superfamily
Z [auth d]	IPR002843	ATPase, V0 complex, C/D subunit	Family
Z [auth d]	IPR016727	ATPase, V0 complex, subunit D	Family
Y [auth U]	IPR004908	ATPase, V1 complex, subunit H	Family
Y [auth U]	IPR016024	Armadillo-type fold	Homologous Superfamily
Y [auth U]	IPR011989	Armadillo-like helical	Homologous Superfamily
Y [auth U]	IPR038497	ATPase, V1 complex, subunit H, C-terminal domain superfamily	Homologous Superfamily
Y [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 a], B [auth g], BA [auth c], C [auth h] A [auth b], AA [auth a], B [auth g], BA [auth c], C [auth h], CA [auth p], D [auth i], DA [auth 0], E [auth j], EA [auth f], F [auth k], FA [auth s], G [auth l], GA [auth e], H [auth m], I [auth n], J [auth o], K [auth 1], L [auth 2], M [auth 3], N [auth 4], O [auth 5], P [auth 7], Q [auth 8], R [auth 9], S [auth Q], T [auth R], U [auth T], V, W [auth X], X [auth 6], Y [auth U], Z [auth d]	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.