9BRS | pdb_00009brs

Intact V-ATPase State 2 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)
M [auth d]	WD40	e9brsd1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: WD40	ECOD (v294.2)
L [auth X]	WD40	e9brsX1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: WD40	ECOD (v294.2)
H [auth U]	WD40	e9brsU1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: WD40	ECOD (v294.2)
G [auth 6]	WD40	e9brs61	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: WD40	ECOD (v294.2)
F [auth V]	WD40	e9brsV1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: WD40	ECOD (v294.2)
E [auth T]	WD40	e9brsT1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: WD40	ECOD (v294.2)
D [auth R]	WD40	e9brsR1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: WD40	ECOD (v294.2)
FA [auth 7]	WD40	e9brs71	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: WD40	ECOD (v294.2)
EA [auth 3]	WD40	e9brs31	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: WD40	ECOD (v294.2)
DA [auth 5]	WD40	e9brs51	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: WD40	ECOD (v294.2)
CA [auth 4]	WD40	e9brs41	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: WD40	ECOD (v294.2)
Z [auth 1]	WD40	e9brs11	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: WD40	ECOD (v294.2)
BA [auth 0]	WD40	e9brs01	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: WD40	ECOD (v294.2)
AA [auth 2]	WD40	e9brs21	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: WD40	ECOD (v294.2)
Y [auth o]	WD40	e9brso1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: WD40	ECOD (v294.2)
X [auth n]	WD40	e9brsn1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: WD40	ECOD (v294.2)
W [auth m]	WD40	e9brsm1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: WD40	ECOD (v294.2)
V [auth l]	WD40	e9brsl1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: WD40	ECOD (v294.2)
U [auth k]	WD40	e9brsk1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: WD40	ECOD (v294.2)
T [auth j]	WD40	e9brsj1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: WD40	ECOD (v294.2)
S [auth i]	WD40	e9brsi1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: WD40	ECOD (v294.2)
R [auth h]	WD40	e9brsh1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: WD40	ECOD (v294.2)
Q [auth g]	WD40	e9brsg1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: WD40	ECOD (v294.2)
P [auth b]	WD40	e9brsb1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: WD40	ECOD (v294.2)
C [auth Q]	WD40	e9brsQ1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: WD40	ECOD (v294.2)
B [auth 9]	WD40	e9brs91	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: WD40	ECOD (v294.2)
A [auth 8]	WD40	e9brs81	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
L [auth X]	PF01990	ATP synthase (F/14-kDa) subunit (ATP-synt_F)	ATP synthase (F/14-kDa) subunit	-	Family
H [auth U]	PF11698	V-ATPase subunit H (V-ATPase_H_C)	V-ATPase subunit H	-	Repeat
H [auth U]	PF03224	V-ATPase subunit H (V-ATPase_H_N)	V-ATPase subunit H	-	Repeat
G [auth 6]	PF03223	V-ATPase subunit C (V-ATPase_C)	V-ATPase subunit C	-	Family
D [auth R], E [auth T], F [auth V]	PF03179	Vacuolar (H+)-ATPase G subunit (V-ATPase_G)	Vacuolar (H+)-ATPase G subunit	-	Coiled-coil
FA [auth 7]	PF01813	ATP synthase subunit D (ATP-synt_D)	ATP synthase subunit D	-	Family
CA [auth 4], DA [auth 5], EA [auth 3]	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
CA [auth 4], DA [auth 5], EA [auth 3]	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
CA [auth 4], DA [auth 5], EA [auth 3]	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
AA [auth 2], BA [auth 0], Z [auth 1]	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
AA [auth 2], BA [auth 0], Z [auth 1]	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
AA [auth 2], BA [auth 0], Z [auth 1]	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
AA [auth 2], BA [auth 0], Z [auth 1]	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 [auth 8], B [auth 9], C [auth Q]	PF01991	ATP synthase (E/31 kDa) subunit (vATP-synt_E)	ATP synthase (E/31 kDa) subunit	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

InterPro: Protein Family Classification InterPro Database Homepage

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

Membrane Protein Annotation: mpstruc mpstruc Database Homepage

Chains	Resource Link	Group	Subgroup	Protein
A [auth 8], AA [auth 2], B [auth 9], BA [auth 0], C [auth Q] A [auth 8], AA [auth 2], B [auth 9], BA [auth 0], C [auth Q], CA [auth 4], D [auth R], DA [auth 5], E [auth T], EA [auth 3], F [auth V], FA [auth 7], G [auth 6], H [auth U], I [auth a], J [auth e], K [auth f], L [auth X], M [auth d], N [auth c], O [auth p], P [auth b], Q [auth g], R [auth h], S [auth i], T [auth j], U [auth k], V [auth l], W [auth m], X [auth n], Y [auth o], Z [auth 1]	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.