7FDA | pdb_00007fda

CryoEM Structure of Reconstituted V-ATPase, state1

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations
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)
O	SCOP2B Superfamily	Vacuolar ATP synthase subunit C	8042806	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)
A	Ion_trans	e7fdaA1	A: alpha bundles	X: RNase A-like	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Ion_trans	ECOD (develop294)
C	Glyco_transf_41	e7fdaC1	A: alpha bundles	X: RNase A-like	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Glyco_transf_41	ECOD (develop294)
E	Glyco_transf_41	e7fdaE1	A: alpha bundles	X: RNase A-like	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Glyco_transf_41	ECOD (develop294)
G	Glyco_hydro_65N	e7fdaG1	A: alpha bundles	X: RNase A-like	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Glyco_hydro_65N	ECOD (develop294)
I	Glyco_hydro_65N	e7fdaI1	A: alpha bundles	X: RNase A-like	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Glyco_hydro_65N	ECOD (develop294)
K	Glyco_hydro_65N	e7fdaK1	A: alpha bundles	X: RNase A-like	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Glyco_hydro_65N	ECOD (develop294)
BA [auth c]	Glyco_hydro_65N	e7fdac1	A: alpha bundles	X: RNase A-like	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Glyco_hydro_65N	ECOD (develop294)
U [auth V]	Glyco_hydro_65N	e7fdaV1	A: alpha bundles	X: RNase A-like	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Glyco_hydro_65N	ECOD (develop294)
W [auth X]	Glyco_hydro_65N	e7fdaX1	A: alpha bundles	X: RNase A-like	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Glyco_hydro_65N	ECOD (develop294)
X [auth Y]	Glyco_hydro_65N	e7fdaY1	A: alpha bundles	X: RNase A-like	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Glyco_hydro_65N	ECOD (develop294)
Z [auth a]	Glyco_hydro_65N	e7fdaa1	A: alpha bundles	X: RNase A-like	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Glyco_hydro_65N	ECOD (develop294)
Y [auth Z]	Glyco_hydro_65N	e7fdaZ1	A: alpha bundles	X: RNase A-like	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Glyco_hydro_65N	ECOD (develop294)
V [auth W]	Glyco_hydro_65N	e7fdaW1	A: alpha bundles	X: RNase A-like	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Glyco_hydro_65N	ECOD (develop294)
AA [auth b]	Glyco_hydro_65N	e7fdab1	A: alpha bundles	X: RNase A-like	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Glyco_hydro_65N	ECOD (develop294)
P	Glyco_hydro_65N	e7fdaP1	A: alpha bundles	X: RNase A-like	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Glyco_hydro_65N	ECOD (develop294)
O	Glyco_hydro_65N	e7fdaO1	A: alpha bundles	X: RNase A-like	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Glyco_hydro_65N	ECOD (develop294)
N	Glyco_hydro_65N	e7fdaN1	A: alpha bundles	X: RNase A-like	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Glyco_hydro_65N	ECOD (develop294)
M	Glyco_hydro_65N	e7fdaM1	A: alpha bundles	X: RNase A-like	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Glyco_hydro_65N	ECOD (develop294)
H	Glyco_hydro_65N	e7fdaH1	A: alpha bundles	X: RNase A-like	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Glyco_hydro_65N	ECOD (develop294)
J	Glyco_hydro_65N	e7fdaJ1	A: alpha bundles	X: RNase A-like	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Glyco_hydro_65N	ECOD (develop294)
L	Glyco_hydro_65N	e7fdaL1	A: alpha bundles	X: RNase A-like	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Glyco_hydro_65N	ECOD (develop294)
B	Glyco_hydro_65N	e7fdaB1	A: alpha bundles	X: RNase A-like	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Glyco_hydro_65N	ECOD (develop294)
D	Glyco_hydro_65N	e7fdaD1	A: alpha bundles	X: RNase A-like	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Glyco_hydro_65N	ECOD (develop294)
F	Glyco_hydro_65N	e7fdaF1	A: alpha bundles	X: RNase A-like	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Glyco_hydro_65N	ECOD (develop294)
T [auth U]	Glyco_hydro_65N	e7fdaU1	A: alpha bundles	X: RNase A-like	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Glyco_hydro_65N	ECOD (develop294)
R [auth S]	Ion_trans	e7fdaS1	A: alpha bundles	X: RNase A-like	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Ion_trans	ECOD (develop294)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, C, E	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, C, E	PF20520	V0 complex accessory subunit Ac45/VOA1 transmembrane domain (Ac45-VOA1_TM)	V0 complex accessory subunit Ac45/VOA1 transmembrane domain	This entry represents the transmembrane domain from ER/Golgi membrane proteins including V0 complex accessory subunit Ac45 (ATP6AP1, also known as V-type proton ATPase subunit S1) from animals and the yeast homologue V0 assembly protein 1 (VOA1) whic ...	This entry represents the transmembrane domain from ER/Golgi membrane proteins including V0 complex accessory subunit Ac45 (ATP6AP1, also known as V-type proton ATPase subunit S1) from animals and the yeast homologue V0 assembly protein 1 (VOA1) which are essential for V0 ATPase assembly, stability and function [1,2]. In humans, mutations of ATP6AP1 cause immunodeficiency with hypogammaglobulinemia, hepatopathy and neurocognitive abnormalities [3]. This entry also includes ER membrane BIG1 proteins from yeast, involved in cell wall biogenesis.	Domain
A, C, E	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, C, E	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, C, E	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, C, E	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
G, I, K	PF01991	ATP synthase (E/31 kDa) subunit (vATP-synt_E)	ATP synthase (E/31 kDa) subunit	-	Family
S [auth T]	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
AA [auth b], BA [auth c], U [auth V], V [auth W], W [auth X], AA [auth b], BA [auth c], U [auth V], V [auth W], W [auth X], X [auth Y], Y [auth Z], Z [auth a]	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
Q	PF01496	V-type ATPase 116kDa subunit family (V_ATPase_I)	V-type ATPase 116kDa subunit family	-	Family
P	PF11698	V-ATPase subunit H (V-ATPase_H_C)	V-ATPase subunit H	-	Repeat
P	PF03224	V-ATPase subunit H (V-ATPase_H_N)	V-ATPase subunit H	-	Repeat
O	PF03223	V-ATPase subunit C (V-ATPase_C)	V-ATPase subunit C	-	Family
N	PF01990	ATP synthase (F/14-kDa) subunit (ATP-synt_F)	ATP synthase (F/14-kDa) subunit	-	Family
M	PF01813	ATP synthase subunit D (ATP-synt_D)	ATP synthase subunit D	-	Family
H, J, L	PF03179	Vacuolar (H+)-ATPase G subunit (V-ATPase_G)	Vacuolar (H+)-ATPase G subunit	-	Coiled-coil
B, D, 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
B, D, F	PF05493	ATP synthase subunit H (ATP_synt_H)	ATP synthase subunit H	-	Family
B, D, 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
B, D, 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
B, D, F	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
T [auth U]	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
R [auth S]	PF01992	ATP synthase (C/AC39) subunit (vATP-synt_AC39)	ATP synthase (C/AC39) subunit	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C, E	IPR036844	Hint domain superfamily	Homologous Superfamily
A, C, E	IPR022878	V-type ATP synthase catalytic alpha chain	Family
A, C, E	IPR006142	Intein	Domain
A, C, E	IPR007868	Hom-end-associated Hint	Domain
A, C, E	IPR004042	Intein DOD homing endonuclease, central region	Domain
A, C, E	IPR024034	ATPase, F1/V1 complex, beta/alpha subunit, C-terminal	Homologous Superfamily
A, C, E	IPR036121	ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain superfamily	Homologous Superfamily
A, C, E	IPR031686	ATPsynthase alpha/beta subunit, barrel-sandwich domain	Domain
A, C, E	IPR006141	Intein N-terminal splicing region	PTM
A, C, E	IPR003586	Hint domain C-terminal	Domain
A, C, E	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
A, C, E	IPR004100	ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain	Domain
A, C, E	IPR030934	Intein C-terminal splicing region	Conserved Site
A, C, E	IPR027434	Homing endonuclease	Homologous Superfamily
A, C, E	IPR023366	ATP synthase subunit alpha, N-terminal domain-like superfamily	Homologous Superfamily
A, C, E	IPR020003	ATPase, alpha/beta subunit, nucleotide-binding domain, active site	Active Site
A, C, E	IPR055190	ATP synthase A/B type, C-terminal domain	Domain
A, C, E	IPR003587	Hint domain N-terminal	Domain
A, C, E	IPR007869	Homing endonuclease PI-Sce	Domain
G, I, K	IPR038495	V-type ATPase subunit E, C-terminal domain superfamily	Homologous Superfamily
G, I, K	IPR002842	V-type ATPase subunit E	Family
S [auth T]	IPR035921	F/V-ATP synthase subunit C superfamily	Homologous Superfamily
S [auth T]	IPR002379	V-ATPase proteolipid subunit C-like domain	Domain
S [auth T]	IPR000245	V-ATPase proteolipid subunit	Family
AA [auth b], BA [auth c], U [auth V], V [auth W], W [auth X], AA [auth b], BA [auth c], U [auth V], V [auth W], W [auth X], X [auth Y], Y [auth Z], Z [auth a]	IPR035921	F/V-ATP synthase subunit C superfamily	Homologous Superfamily
AA [auth b], BA [auth c], U [auth V], V [auth W], W [auth X], AA [auth b], BA [auth c], U [auth V], V [auth W], W [auth X], X [auth Y], Y [auth Z], Z [auth a]	IPR002379	V-ATPase proteolipid subunit C-like domain	Domain
AA [auth b], BA [auth c], U [auth V], V [auth W], W [auth X], AA [auth b], BA [auth c], U [auth V], V [auth W], W [auth X], X [auth Y], Y [auth Z], Z [auth a]	IPR011555	V-ATPase proteolipid subunit C, eukaryotic	Family
AA [auth b], BA [auth c], U [auth V], V [auth W], W [auth X], AA [auth b], BA [auth c], U [auth V], V [auth W], W [auth X], X [auth Y], Y [auth Z], Z [auth a]	IPR000245	V-ATPase proteolipid subunit	Family
DA [auth e]	IPR046756	V-type proton ATPase subunit S1/VOA1, transmembrane domain	Domain
Q	IPR026028	ATPase, V0 complex, subunit 116kDa, eukaryotic	Family
Q	IPR002490	V-type ATPase, V0 complex, 116kDa subunit family	Family
P	IPR004908	ATPase, V1 complex, subunit H	Family
P	IPR016024	Armadillo-type fold	Homologous Superfamily
P	IPR011989	Armadillo-like helical	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
P	IPR004908	ATPase, V1 complex, subunit H	Family
P	IPR016024	Armadillo-type fold	Homologous Superfamily
P	IPR011989	Armadillo-like helical	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
O	IPR036132	Vacuolar ATP synthase subunit C superfamily	Homologous Superfamily
O	IPR004907	ATPase, V1 complex, subunit C	Family
N	IPR036906	ATPase, V1 complex, subunit F superfamily	Homologous Superfamily
N	IPR005772	ATPase, V1 complex, subunit F, eukaryotic	Family
N	IPR008218	ATPase, V1 complex, subunit F	Family
M	IPR002699	ATPase, V1 complex, subunit D	Family
H, J, L	IPR005124	Vacuolar (H+)-ATPase G subunit	Family
B, D, F	IPR000194	ATPase, F1/V1/A1 complex, alpha/beta subunit, nucleotide-binding domain	Domain
B, D, F	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
B, D, F	IPR004100	ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain	Domain
B, D, F	IPR005723	ATPase, V1 complex, subunit B	Family
B, D, F	IPR022879	V-type ATP synthase regulatory subunit B/beta	Family
B, D, F	IPR020003	ATPase, alpha/beta subunit, nucleotide-binding domain, active site	Active Site
B, D, F	IPR055190	ATP synthase A/B type, C-terminal domain	Domain
EA [auth f]	IPR056552	Ribonucl_Kappa	Unknown
EA [auth f]	IPR026770	Ribonuclease kappa	Family
CA [auth d]	IPR008389	ATPase, V0 complex, subunit e1/e2	Family
T [auth U]	IPR035921	F/V-ATP synthase subunit C superfamily	Homologous Superfamily
T [auth U]	IPR002379	V-ATPase proteolipid subunit C-like domain	Domain
T [auth U]	IPR011555	V-ATPase proteolipid subunit C, eukaryotic	Family
T [auth U]	IPR000245	V-ATPase proteolipid subunit	Family
R [auth S]	IPR044911	V-type ATP synthase C/D subunit, domain 3 superfamily	Homologous Superfamily
R [auth S]	IPR002843	ATPase, V0 complex, C/D subunit	Family
R [auth S]	IPR036079	V-type ATP synthase subunit C/D subunit superfamily	Homologous Superfamily
R [auth S]	IPR035067	V-type ATPase subunit C/D	Homologous Superfamily
R [auth S]	IPR016727	ATPase, V0 complex, subunit D	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
P	Pharos: Q9UI12	astrocytic tumor large cell medulloblastoma medulloblastoma Pick disease primitive neuroectodermal tumor atypical teratoid rhabdoid tumor malignant ependymoma oligodendroglioma pilocytic astrocytoma glioblastoma malignant glioma ovarian cancer plasma cell myeloma

Membrane Protein Annotation: OPM OPM Database Homepage

Chains	External Link	Type	Class	Superfamily	Family
A, AA [auth b], B, BA [auth c], C A, AA [auth b], B, BA [auth c], C, CA [auth d], D, DA [auth e], E, EA [auth f], F, G, H, I, J, K, L, M, N, O, P, Q, R [auth S], S [auth T], T [auth U], U [auth V], V [auth W], W [auth X], X [auth Y], Y [auth Z], Z [auth a]	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 b], B, BA [auth c], C A, AA [auth b], B, BA [auth c], C, CA [auth d], D, DA [auth e], E, EA [auth f], F, G, H, I, J, K, L, M, N, O, P, Q, R [auth S], S [auth T], T [auth U], U [auth V], V [auth W], W [auth X], X [auth Y], Y [auth Z], Z [auth a]	PDBTM	Annotated as membrane protein by PDBTM

Membrane Protein Annotation: mpstruc mpstruc Database Homepage

Chains	Resource Link	Group	Subgroup	Protein
A, AA [auth b], B, BA [auth c], C A, AA [auth b], B, BA [auth c], C, CA [auth d], D, DA [auth e], E, EA [auth f], F, G, H, I, J, K, L, M, N, O, P, Q, R [auth S], S [auth T], T [auth U], U [auth V], V [auth W], W [auth X], X [auth Y], Y [auth Z], Z [auth a]	mpstruc	TRANSMEMBRANE PROTEINS: ALPHA-HELICAL	Vacuolar ATPase (V-ATPase)	Complete V-ATPase by cryo-EM, state 1