6VQ7 | pdb_00006vq7

Mammalian V-ATPase from rat brain - composite model of rotational state 2 bound to ADP and SidK (built from focused refinement models)


Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

ChainsTypeFamily Name Domain Identifier Family IdentifierProvenance Source (Version)
GSCOP2B SuperfamilyVacuolar ATP synthase subunit C 8099588 3001744 SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

ChainsFamily NameDomain Identifier ArchitecturePossible HomologyHomologyTopologyFamilyProvenance Source (Version)
Ae6vq7A1 A: Family A G protein-coupled receptor-likeX: Family A G protein-coupled receptor-likeH: Family A G protein-coupled receptor-likeT: CBSF:ECOD (20:10:01)
Be6vq7B1 A: Family A G protein-coupled receptor-likeX: Family A G protein-coupled receptor-likeH: Family A G protein-coupled receptor-likeT: CBSF:ECOD (20:10:01)
Ce6vq7C1 A: Family A G protein-coupled receptor-likeX: Family A G protein-coupled receptor-likeH: Family A G protein-coupled receptor-likeT: CBSF:ECOD (20:10:01)
De6vq7D1 A: Family A G protein-coupled receptor-likeX: Family A G protein-coupled receptor-likeH: Family A G protein-coupled receptor-likeT: CBSF:ECOD (20:10:01)
Ee6vq7E1 A: Family A G protein-coupled receptor-likeX: Family A G protein-coupled receptor-likeH: Family A G protein-coupled receptor-likeT: CBSF:ECOD (20:10:01)
Fe6vq7F1 A: Family A G protein-coupled receptor-likeX: Family A G protein-coupled receptor-likeH: Family A G protein-coupled receptor-likeT: CBSF:ECOD (20:10:01)
Ge6vq7G1 A: Family A G protein-coupled receptor-likeX: Family A G protein-coupled receptor-likeH: Family A G protein-coupled receptor-likeT: PXF:ECOD (20:10:01)
He6vq7H1 A: Family A G protein-coupled receptor-likeX: Family A G protein-coupled receptor-likeH: Family A G protein-coupled receptor-likeT: CBSF:ECOD (20:10:01)
Ie6vq7I1 A: Family A G protein-coupled receptor-likeX: Family A G protein-coupled receptor-likeH: Family A G protein-coupled receptor-likeT: CBSF:ECOD (20:10:01)
Je6vq7J1 A: Family A G protein-coupled receptor-likeX: Family A G protein-coupled receptor-likeH: Family A G protein-coupled receptor-likeT: CBSF:ECOD (20:10:01)
Ke6vq7K1 A: Family A G protein-coupled receptor-likeX: Family A G protein-coupled receptor-likeH: Family A G protein-coupled receptor-likeT: CBSF:ECOD (20:10:01)
Le6vq7L1 A: Family A G protein-coupled receptor-likeX: Family A G protein-coupled receptor-likeH: Family A G protein-coupled receptor-likeT: CBSF:ECOD (20:10:01)
Me6vq7M1 A: Family A G protein-coupled receptor-likeX: Family A G protein-coupled receptor-likeH: Family A G protein-coupled receptor-likeT: CBSF:ECOD (20:10:01)
Ne6vq7N1 A: Family A G protein-coupled receptor-likeX: Family A G protein-coupled receptor-likeH: Family A G protein-coupled receptor-likeT: CBSF:ECOD (20:10:01)
Oe6vq7O1 A: Family A G protein-coupled receptor-likeX: Family A G protein-coupled receptor-likeH: Family A G protein-coupled receptor-likeT: CBSF:ECOD (20:10:01)
P [auth Q]e6vq7Q1 A: Family A G protein-coupled receptor-likeX: Family A G protein-coupled receptor-likeH: Family A G protein-coupled receptor-likeT: CBSF:ECOD (20:10:01)
Q [auth R]e6vq7R1 A: Family A G protein-coupled receptor-likeX: Family A G protein-coupled receptor-likeH: Family A G protein-coupled receptor-likeT: CBSF:ECOD (20:10:01)
R [auth S]e6vq7S1 A: Family A G protein-coupled receptor-likeX: Family A G protein-coupled receptor-likeH: Family A G protein-coupled receptor-likeT: CBSF:ECOD (20:10:01)
V [auth d]e6vq7d1 A: Family A G protein-coupled receptor-likeX: Family A G protein-coupled receptor-likeH: Family A G protein-coupled receptor-likeT: CBSF:ECOD (20:10:01)
AA [auth i]e6vq7i1 A: Family A G protein-coupled receptor-likeX: Family A G protein-coupled receptor-likeH: Family A G protein-coupled receptor-likeT: CBSF:ECOD (20:10:01)
BA [auth j]e6vq7j1 A: Family A G protein-coupled receptor-likeX: Family A G protein-coupled receptor-likeH: Family A G protein-coupled receptor-likeT: CBSF:ECOD (20:10:01)
DA [auth l]e6vq7l1 A: Family A G protein-coupled receptor-likeX: Family A G protein-coupled receptor-likeH: Family A G protein-coupled receptor-likeT: CBSF:ECOD (20:10:01)
EA [auth m]e6vq7m1 A: Family A G protein-coupled receptor-likeX: Family A G protein-coupled receptor-likeH: Family A G protein-coupled receptor-likeT: CBSF:ECOD (20:10:01)
FA [auth n]e6vq7n1 A: Family A G protein-coupled receptor-likeX: Family A G protein-coupled receptor-likeH: Family A G protein-coupled receptor-likeT: CBSF:ECOD (20:10:01)
GA [auth o]e6vq7o1 A: Family A G protein-coupled receptor-likeX: Family A G protein-coupled receptor-likeH: Family A G protein-coupled receptor-likeT: CBSF:ECOD (20:10:01)
Y [auth g]e6vq7g1 A: Family A G protein-coupled receptor-likeX: Family A G protein-coupled receptor-likeH: Family A G protein-coupled receptor-likeT: CBSF:ECOD (20:10:01)
Z [auth h]e6vq7h1 A: Family A G protein-coupled receptor-likeX: Family A G protein-coupled receptor-likeH: Family A G protein-coupled receptor-likeT: CBSF:ECOD (20:10:01)
CA [auth k]e6vq7k1 A: Family A G protein-coupled receptor-likeX: Family A G protein-coupled receptor-likeH: Family A G protein-coupled receptor-likeT: CBSF:ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

ChainDomainClassArchitectureTopologyHomologyProvenance Source (Version)
A3.40.50.300 Alpha Beta 3-Layer(aba) Sandwich Rossmann fold P-loop containing nucleotide triphosphate hydrolasesCATH (utative)
A2.40.50.100 Mainly Beta Beta Barrel OB fold (Dihydrolipoamide Acetyltransferase, E2P) RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domainCATH (utative)
B3.40.50.300 Alpha Beta 3-Layer(aba) Sandwich Rossmann fold P-loop containing nucleotide triphosphate hydrolasesCATH (utative)
B2.40.50.100 Mainly Beta Beta Barrel OB fold (Dihydrolipoamide Acetyltransferase, E2P) RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domainCATH (utative)
C3.40.50.300 Alpha Beta 3-Layer(aba) Sandwich Rossmann fold P-loop containing nucleotide triphosphate hydrolasesCATH (utative)
C2.40.50.100 Mainly Beta Beta Barrel OB fold (Dihydrolipoamide Acetyltransferase, E2P) RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domainCATH (utative)
D3.40.50.12240 Alpha Beta 3-Layer(aba) Sandwich Rossmann fold CATH (utative)
E3.40.50.12240 Alpha Beta 3-Layer(aba) Sandwich Rossmann fold CATH (utative)
F3.40.50.12240 Alpha Beta 3-Layer(aba) Sandwich Rossmann fold CATH (utative)
G1.20.1460.10 Mainly Alpha Up-down Bundle subunit c (vma5p) of the yeast v-atpase, domain 2 subunit c (vma5p) of the yeast v-atpase, domain 2CATH (utative)
G3.30.70.100 Alpha Beta 2-Layer Sandwich Alpha-Beta Plaits CATH (utative)
H1.10.287.3240 Mainly Alpha Orthogonal Bundle Helix Hairpins CATH (utative)
I3.30.2320.30 Alpha Beta 2-Layer Sandwich hypothetical protein PF0899 fold ATP synthase, E subunit, C-terminalCATH (utative)
J3.30.2320.30 Alpha Beta 2-Layer Sandwich hypothetical protein PF0899 fold ATP synthase, E subunit, C-terminalCATH (utative)
K3.30.2320.30 Alpha Beta 2-Layer Sandwich hypothetical protein PF0899 fold ATP synthase, E subunit, C-terminalCATH (utative)
L3.40.50.10580 Alpha Beta 3-Layer(aba) Sandwich Rossmann fold ATPase, V1 complex, subunit FCATH (utative)

Protein Family Annotation Pfam Database Homepage

ChainsAccessionNameDescriptionCommentsSource
A, B, C
PF00006ATP synthase alpha/beta family, nucleotide-binding domain (ATP-synt_ab)ATP synthase alpha/beta family, nucleotide-binding domainThis entry includes the ATP synthase alpha and beta subunits, the ATP synthase associated with flagella and the termination factor Rho. Domain
A, B, C
PF20520V0 complex accessory subunit Ac45/VOA1 transmembrane domain (Ac45-VOA1_TM)V0 complex accessory subunit Ac45/VOA1 transmembrane domainThis 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, B, C
PF22919C-terminal domain of V and A type ATP synthase (ATP-synt_VA_C)C-terminal domain of V and A type ATP synthaseThis entry represents a small alpha helical domain found at the C-terminus of a variety of ATP synthases. Domain
A, B, C
PF16886ATPsynthase alpha/beta subunit barrel-sandwich domain (ATP-synt_ab_Xtn)ATPsynthase alpha/beta subunit barrel-sandwich domainThis 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
PF01496V-type ATPase 116kDa subunit family (V_ATPase_I)V-type ATPase 116kDa subunit family- Family
A, B, C
PF02874ATP synthase alpha/beta family, beta-barrel domain (ATP-synt_ab_N)ATP synthase alpha/beta family, beta-barrel domainThis family includes the ATP synthase alpha and beta subunits the ATP synthase associated with flagella. Domain
D, E, F
PF05493ATP synthase subunit H (ATP_synt_H)ATP synthase subunit H- Family
D, E, F
PF00006ATP synthase alpha/beta family, nucleotide-binding domain (ATP-synt_ab)ATP synthase alpha/beta family, nucleotide-binding domainThis entry includes the ATP synthase alpha and beta subunits, the ATP synthase associated with flagella and the termination factor Rho. Domain
D, E, F
PF22919C-terminal domain of V and A type ATP synthase (ATP-synt_VA_C)C-terminal domain of V and A type ATP synthaseThis entry represents a small alpha helical domain found at the C-terminus of a variety of ATP synthases. Domain
D, E, F
PF02874ATP synthase alpha/beta family, beta-barrel domain (ATP-synt_ab_N)ATP synthase alpha/beta family, beta-barrel domainThis family includes the ATP synthase alpha and beta subunits the ATP synthase associated with flagella. Domain
PF03223V-ATPase subunit C (V-ATPase_C)V-ATPase subunit C- Family
PF00137ATP synthase subunit C (ATP-synt_C)ATP synthase subunit CThis 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
PF01813ATP synthase subunit D (ATP-synt_D)ATP synthase subunit D- Family
PF00137ATP synthase subunit C (ATP-synt_C)ATP synthase subunit CThis 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
PF01991ATP synthase (E/31 kDa) subunit (vATP-synt_E)ATP synthase (E/31 kDa) subunit- Family
I, J, K
PF00137ATP synthase subunit C (ATP-synt_C)ATP synthase subunit CThis 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
PF01990ATP synthase (F/14-kDa) subunit (ATP-synt_F)ATP synthase (F/14-kDa) subunit- Family
PF00137ATP synthase subunit C (ATP-synt_C)ATP synthase subunit CThis 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
PF03179Vacuolar (H+)-ATPase G subunit (V-ATPase_G)Vacuolar (H+)-ATPase G subunit- Coiled-coil
M, N, O
PF00137ATP synthase subunit C (ATP-synt_C)ATP synthase subunit CThis 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

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
A, B, C
ATPase H+-transporting V1 subunit A
D, E, F
V-type proton ATPase subunit B, brain isoform
V-type proton ATPase subunit C 1
ATPase H+-transporting V1 subunit D
I, J, K
V-type proton ATPase subunit E 1
V-type proton ATPase subunit F
M, N, O
V-type proton ATPase subunit G
P [auth Q],
Q [auth R],
R [auth S]
Effector protein SidK- -
S [auth a]V-type proton ATPase 116 kDa subunit a isoform 1
T [auth b]ATPase, H+ transporting, V0 subunit B (Predicted), isoform CRA_a -
U [auth c]V-type proton ATPase subunit S1
V [auth d]V-type proton ATPase subunit
W [auth e]V-type proton ATPase subunit e 2
X [auth f]Ribonuclease K
V-type proton ATPase 16 kDa proteolipid subunit
HA [auth p]Renin receptor

InterPro: Protein Family Classification InterPro Database Homepage

ChainsAccessionNameType
A, B, C
IPR004100ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domainDomain
A, B, C
IPR022878V-type ATP synthase catalytic alpha chainFamily
A, B, C
IPR024034ATPase, F1/V1 complex, beta/alpha subunit, C-terminalHomologous Superfamily
A, B, C
IPR036121ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain superfamilyHomologous Superfamily
A, B, C
IPR031686ATPsynthase alpha/beta subunit, barrel-sandwich domainDomain
A, B, C
IPR023366ATP synthase subunit alpha, N-terminal domain-like superfamilyHomologous Superfamily
A, B, C
IPR020003ATPase, alpha/beta subunit, nucleotide-binding domain, active siteActive Site
A, B, C
IPR000194ATPase, F1/V1/A1 complex, alpha/beta subunit, nucleotide-binding domainDomain
A, B, C
IPR055190ATP synthase A/B type, C-terminal domainDomain
A, B, C
IPR005725ATPase, V1 complex, subunit AFamily
A, B, C
IPR027417P-loop containing nucleoside triphosphate hydrolaseHomologous Superfamily
D, E, F
IPR004100ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domainDomain
D, E, F
IPR005723ATPase, V1 complex, subunit BFamily
D, E, F
IPR022879V-type ATP synthase regulatory subunit B/betaFamily
D, E, F
IPR020003ATPase, alpha/beta subunit, nucleotide-binding domain, active siteActive Site
D, E, F
IPR000194ATPase, F1/V1/A1 complex, alpha/beta subunit, nucleotide-binding domainDomain
D, E, F
IPR055190ATP synthase A/B type, C-terminal domainDomain
D, E, F
IPR027417P-loop containing nucleoside triphosphate hydrolaseHomologous Superfamily
IPR004907ATPase, V1 complex, subunit CFamily
IPR036132Vacuolar ATP synthase subunit C superfamilyHomologous Superfamily
IPR002699ATPase, V1 complex, subunit DFamily
I, J, K
IPR038495V-type ATPase subunit E, C-terminal domain superfamilyHomologous Superfamily
I, J, K
IPR002842V-type ATPase subunit EFamily
IPR005772ATPase, V1 complex, subunit F, eukaryoticFamily
IPR036906ATPase, V1 complex, subunit F superfamilyHomologous Superfamily
IPR008218ATPase, V1 complex, subunit FFamily
M, N, O
IPR005124Vacuolar (H+)-ATPase G subunitFamily
S [auth a]IPR026028ATPase, V0 complex, subunit 116kDa, eukaryoticFamily
S [auth a]IPR002490V-type ATPase, V0 complex, 116kDa subunit familyFamily
T [auth b]IPR035921F/V-ATP synthase subunit C superfamilyHomologous Superfamily
T [auth b]IPR000245V-ATPase proteolipid subunitFamily
T [auth b]IPR002379V-ATPase proteolipid subunit C-like domainDomain
U [auth c]IPR046755V-type proton ATPase subunit S1, luminal domainDomain
U [auth c]IPR008388V0 complex accessory subunit Ac45Family
U [auth c]IPR046756V-type proton ATPase subunit S1/VOA1, transmembrane domainDomain
V [auth d]IPR016727ATPase, V0 complex, subunit DFamily
V [auth d]IPR044911V-type ATP synthase C/D subunit, domain 3 superfamilyHomologous Superfamily
V [auth d]IPR002843ATPase, V0 complex, C/D subunitFamily
V [auth d]IPR036079V-type ATP synthase subunit C/D subunit superfamilyHomologous Superfamily
V [auth d]IPR035067V-type ATPase subunit C/DHomologous Superfamily
W [auth e]IPR017385ATPase, V0 complex, subunit e1/e2, metazoaFamily
W [auth e]IPR008389ATPase, V0 complex, subunit e1/e2Family
X [auth f]IPR056552Ribonucl_KappaUnknown
X [auth f]IPR026770Ribonuclease kappaFamily
IPR035921F/V-ATP synthase subunit C superfamilyHomologous Superfamily
IPR002379V-ATPase proteolipid subunit C-like domainDomain
IPR011555V-ATPase proteolipid subunit C, eukaryoticFamily
IPR000245V-ATPase proteolipid subunitFamily
HA [auth p]IPR056780Renin receptor-like, C-terminal transmembrane spanning segmentDomain
HA [auth p]IPR012493Renin receptor-likeFamily
HA [auth p]IPR057318Renin receptor, N-terminal domainDomain