6WM4 | pdb_00006wm4

Human V-ATPase in state 3 with SidK and ADP


Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

ChainsTypeFamily Name Domain Identifier Family IdentifierProvenance Source (Version)
B [auth O]SCOP2 FamilyVacuolar ATP synthase subunit C 8101528 4003895 SCOP2 (2022-06-29)
B [auth O]SCOP2 SuperfamilyVacuolar ATP synthase subunit C 8101529 3001744 SCOP2 (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

ChainsFamily NameDomain Identifier ArchitecturePossible HomologyHomologyTopologyFamilyProvenance Source (Version)
B [auth O]Glycos_transf_3e6wm4O1 A: alpha bundlesX: CNF1/YfiH-like putative cysteine hydrolasesH: RIFT-relatedT: FMN-binding split barrel 2F: Glycos_transf_3ECOD (develop294)
G [auth H]LRR_1,LRR_8e6wm4H1 A: alpha bundlesX: cradle loop barrelH: N-terminal domain of poxinT: N-terminal domain of poxinF: LRR_1,LRR_8ECOD (develop294)
E [auth I]LRR_1,LRR_8e6wm4I1 A: alpha bundlesX: cradle loop barrelH: N-terminal domain of poxinT: N-terminal domain of poxinF: LRR_1,LRR_8ECOD (develop294)
C [auth J]LRR_1,LRR_8e6wm4J1 A: alpha bundlesX: cradle loop barrelH: N-terminal domain of poxinT: N-terminal domain of poxinF: LRR_1,LRR_8ECOD (develop294)
H [auth K]LRR_1,LRR_8e6wm4K1 A: alpha bundlesX: cradle loop barrelH: N-terminal domain of poxinT: N-terminal domain of poxinF: LRR_1,LRR_8ECOD (develop294)
F [auth L]LRR_1,LRR_8e6wm4L1 A: alpha bundlesX: cradle loop barrelH: N-terminal domain of poxinT: N-terminal domain of poxinF: LRR_1,LRR_8ECOD (develop294)
D [auth M]LRR_1,LRR_8e6wm4M1 A: alpha bundlesX: cradle loop barrelH: N-terminal domain of poxinT: N-terminal domain of poxinF: LRR_1,LRR_8ECOD (develop294)
M [auth A]LRR_1,LRR_8e6wm4A1 A: alpha bundlesX: cradle loop barrelH: N-terminal domain of poxinT: N-terminal domain of poxinF: LRR_1,LRR_8ECOD (develop294)
L [auth C]LRR_1,LRR_8e6wm4C1 A: alpha bundlesX: cradle loop barrelH: N-terminal domain of poxinT: N-terminal domain of poxinF: LRR_1,LRR_8ECOD (develop294)
K [auth B]LRR_1,LRR_8e6wm4B1 A: alpha bundlesX: cradle loop barrelH: N-terminal domain of poxinT: N-terminal domain of poxinF: LRR_1,LRR_8ECOD (develop294)
P [auth D]LRR_1,LRR_8e6wm4D1 A: alpha bundlesX: cradle loop barrelH: N-terminal domain of poxinT: N-terminal domain of poxinF: LRR_1,LRR_8ECOD (develop294)
O [auth F]LRR_1,LRR_8e6wm4F1 A: alpha bundlesX: cradle loop barrelH: N-terminal domain of poxinT: N-terminal domain of poxinF: LRR_1,LRR_8ECOD (develop294)
N [auth E]LRR_1,LRR_8e6wm4E1 A: alpha bundlesX: cradle loop barrelH: N-terminal domain of poxinT: N-terminal domain of poxinF: LRR_1,LRR_8ECOD (develop294)
T [auth G]LRR_1,LRR_8e6wm4G1 A: alpha bundlesX: cradle loop barrelH: N-terminal domain of poxinT: N-terminal domain of poxinF: LRR_1,LRR_8ECOD (develop294)
U [auth N]LRR_1,LRR_8e6wm4N1 A: alpha bundlesX: cradle loop barrelH: N-terminal domain of poxinT: N-terminal domain of poxinF: LRR_1,LRR_8ECOD (develop294)
Z [auth 2]LRR_1,LRR_8e6wm421 A: alpha bundlesX: cradle loop barrelH: N-terminal domain of poxinT: N-terminal domain of poxinF: LRR_1,LRR_8ECOD (develop294)
Y [auth 1]LRR_1,LRR_8e6wm411 A: alpha bundlesX: cradle loop barrelH: N-terminal domain of poxinT: N-terminal domain of poxinF: LRR_1,LRR_8ECOD (develop294)
GA [auth 9]LRR_1,LRR_8e6wm491 A: alpha bundlesX: cradle loop barrelH: N-terminal domain of poxinT: N-terminal domain of poxinF: LRR_1,LRR_8ECOD (develop294)
FA [auth 8]LRR_1,LRR_8e6wm481 A: alpha bundlesX: cradle loop barrelH: N-terminal domain of poxinT: N-terminal domain of poxinF: LRR_1,LRR_8ECOD (develop294)
EA [auth 7]LRR_1,LRR_8e6wm471 A: alpha bundlesX: cradle loop barrelH: N-terminal domain of poxinT: N-terminal domain of poxinF: LRR_1,LRR_8ECOD (develop294)
DA [auth 6]LRR_1,LRR_8e6wm461 A: alpha bundlesX: cradle loop barrelH: N-terminal domain of poxinT: N-terminal domain of poxinF: LRR_1,LRR_8ECOD (develop294)
CA [auth 5]LRR_1,LRR_8e6wm451 A: alpha bundlesX: cradle loop barrelH: N-terminal domain of poxinT: N-terminal domain of poxinF: LRR_1,LRR_8ECOD (develop294)
BA [auth 4]LRR_1,LRR_8e6wm441 A: alpha bundlesX: cradle loop barrelH: N-terminal domain of poxinT: N-terminal domain of poxinF: LRR_1,LRR_8ECOD (develop294)
AA [auth 3]LRR_1,LRR_8e6wm431 A: alpha bundlesX: cradle loop barrelH: N-terminal domain of poxinT: N-terminal domain of poxinF: LRR_1,LRR_8ECOD (develop294)
HA [auth Q]LRR_1,LRR_8e6wm4Q1 A: alpha bundlesX: cradle loop barrelH: N-terminal domain of poxinT: N-terminal domain of poxinF: LRR_1,LRR_8ECOD (develop294)
IA [auth P]Glycos_transf_3e6wm4P1 A: alpha bundlesX: CNF1/YfiH-like putative cysteine hydrolasesH: RIFT-relatedT: FMN-binding split barrel 2F: Glycos_transf_3ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Protein Family Annotation Pfam Database Homepage

ChainsAccessionNameDescriptionCommentsSource
A [auth R]PF01496V-type ATPase 116kDa subunit family (V_ATPase_I)V-type ATPase 116kDa subunit family- Family
B [auth O]PF03223V-ATPase subunit C (V-ATPase_C)V-ATPase subunit C- Family
C [auth J],
E [auth I],
G [auth H]
PF01991ATP synthase (E/31 kDa) subunit (vATP-synt_E)ATP synthase (E/31 kDa) subunit- Family
D [auth M],
F [auth L],
H [auth K]
PF03179Vacuolar (H+)-ATPase G subunit (V-ATPase_G)Vacuolar (H+)-ATPase G subunit- Coiled-coil
I [auth S]PF05493ATP synthase subunit H (ATP_synt_H)ATP synthase subunit H- Family
K [auth B],
L [auth C],
M [auth A]
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
K [auth B],
L [auth C],
M [auth A]
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
K [auth B],
L [auth C],
M [auth A]
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
K [auth B],
L [auth C],
M [auth A]
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
N [auth E],
O [auth F],
P [auth D]
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
N [auth E],
O [auth F],
P [auth D]
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
N [auth E],
O [auth F],
P [auth D]
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
T [auth G]PF01813ATP synthase subunit D (ATP-synt_D)ATP synthase subunit D- Family
U [auth N]PF01990ATP synthase (F/14-kDa) subunit (ATP-synt_F)ATP synthase (F/14-kDa) subunit- Family
V [auth U]PF05827V-type proton ATPase subunit S1, luminal domain (VAS1_LD)V-type proton ATPase subunit S1, luminal domainThis entry represents the luminal domain (LD) found in eukaryotic V-type proton ATPase subunit S1 involved in V-ATPase V0 assembly, including Ac45 subunit (ATP6AP1) [1,2]. This domain folds as a globular beta-prism structure which is structurally sim ...This entry represents the luminal domain (LD) found in eukaryotic V-type proton ATPase subunit S1 involved in V-ATPase V0 assembly, including Ac45 subunit (ATP6AP1) [1,2]. This domain folds as a globular beta-prism structure which is structurally similar to LAMP1-3, thus, the LD domain of Ac45 is an evolutionarily conserved member of the LAMP family [2]. Ac45 is an ER membrane protein that guides the V-type ATPase into specialised subcellular compartments [3] and is critical for Vo complex assembly as it connects to multiple Vo subunits and phospholipids in the c-ring [2]. Missense mutations in the X-linked ATP6AP1 gene cause immunodeficiency in males that leads to recurrent bacterial infection, hepatopathy, cognitive impairment, and abnormal protein glycosylation [2].
Domain
V [auth U]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
X [auth 0]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
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
HA [auth Q]PF01992ATP synthase (C/AC39) subunit (vATP-synt_AC39)ATP synthase (C/AC39) subunit- Family
IA [auth P]PF11698V-ATPase subunit H (V-ATPase_H_C)V-ATPase subunit H- Repeat
IA [auth P]PF03224V-ATPase subunit H (V-ATPase_H_N)V-ATPase subunit H- Repeat

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
A [auth R]V-type proton ATPase 116 kDa subunit a isoform 1
B [auth O]V-type proton ATPase subunit C 1
C [auth J],
E [auth I],
G [auth H]
V-type proton ATPase subunit E 1
D [auth M],
F [auth L],
H [auth K]
V-type proton ATPase subunit G 1
I [auth S]V-type proton ATPase subunit e 1
J [auth T]Ribonuclease kappa
K [auth B],
L [auth C],
M [auth A]
V-type proton ATPase catalytic subunit A
N [auth E],
O [auth F],
P [auth D]
V-type proton ATPase subunit B, brain isoform
Q [auth Y],
R [auth Z],
S [auth X]
SidK- -
T [auth G]V-type proton ATPase subunit D
U [auth N]V-type proton ATPase subunit F
V [auth U]V-type proton ATPase subunit S1
W [auth V]Renin receptor
X [auth 0]V-type proton ATPase 21 kDa proteolipid subunit
V-type proton ATPase 16 kDa proteolipid subunit
HA [auth Q]V-type proton ATPase subunit d 1
IA [auth P]V-type proton ATPase subunit H

InterPro: Protein Family Classification InterPro Database Homepage

ChainsAccessionNameType
A [auth R]IPR026028ATPase, V0 complex, subunit 116kDa, eukaryoticFamily
A [auth R]IPR002490V-type ATPase, V0 complex, 116kDa subunit familyFamily
B [auth O]IPR036132Vacuolar ATP synthase subunit C superfamilyHomologous Superfamily
B [auth O]IPR004907ATPase, V1 complex, subunit CFamily
C [auth J],
E [auth I],
G [auth H]
IPR038495V-type ATPase subunit E, C-terminal domain superfamilyHomologous Superfamily
C [auth J],
E [auth I],
G [auth H]
IPR002842V-type ATPase subunit EFamily
D [auth M],
F [auth L],
H [auth K]
IPR005124Vacuolar (H+)-ATPase G subunitFamily
I [auth S]IPR017385ATPase, V0 complex, subunit e1/e2, metazoaFamily
I [auth S]IPR008389ATPase, V0 complex, subunit e1/e2Family
J [auth T]IPR056552Ribonucl_KappaUnknown
J [auth T]IPR026770Ribonuclease kappaFamily
K [auth B],
L [auth C],
M [auth A]
IPR022878V-type ATP synthase catalytic alpha chainFamily
K [auth B],
L [auth C],
M [auth A]
IPR024034ATPase, F1/V1 complex, beta/alpha subunit, C-terminalHomologous Superfamily
K [auth B],
L [auth C],
M [auth A]
IPR036121ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain superfamilyHomologous Superfamily
K [auth B],
L [auth C],
M [auth A]
IPR031686ATPsynthase alpha/beta subunit, barrel-sandwich domainDomain
K [auth B],
L [auth C],
M [auth A]
IPR000194ATPase, F1/V1/A1 complex, alpha/beta subunit, nucleotide-binding domainDomain
K [auth B],
L [auth C],
M [auth A]
IPR005725ATPase, V1 complex, subunit AFamily
K [auth B],
L [auth C],
M [auth A]
IPR027417P-loop containing nucleoside triphosphate hydrolaseHomologous Superfamily
K [auth B],
L [auth C],
M [auth A]
IPR004100ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domainDomain
K [auth B],
L [auth C],
M [auth A]
IPR023366ATP synthase subunit alpha, N-terminal domain-like superfamilyHomologous Superfamily
K [auth B],
L [auth C],
M [auth A]
IPR020003ATPase, alpha/beta subunit, nucleotide-binding domain, active siteActive Site
K [auth B],
L [auth C],
M [auth A]
IPR055190ATP synthase A/B type, C-terminal domainDomain
N [auth E],
O [auth F],
P [auth D]
IPR000194ATPase, F1/V1/A1 complex, alpha/beta subunit, nucleotide-binding domainDomain
N [auth E],
O [auth F],
P [auth D]
IPR027417P-loop containing nucleoside triphosphate hydrolaseHomologous Superfamily
N [auth E],
O [auth F],
P [auth D]
IPR004100ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domainDomain
N [auth E],
O [auth F],
P [auth D]
IPR005723ATPase, V1 complex, subunit BFamily
N [auth E],
O [auth F],
P [auth D]
IPR022879V-type ATP synthase regulatory subunit B/betaFamily
N [auth E],
O [auth F],
P [auth D]
IPR020003ATPase, alpha/beta subunit, nucleotide-binding domain, active siteActive Site
N [auth E],
O [auth F],
P [auth D]
IPR055190ATP synthase A/B type, C-terminal domainDomain
T [auth G]IPR002699ATPase, V1 complex, subunit DFamily
U [auth N]IPR008218ATPase, V1 complex, subunit FFamily
U [auth N]IPR036906ATPase, V1 complex, subunit F superfamilyHomologous Superfamily
U [auth N]IPR005772ATPase, V1 complex, subunit F, eukaryoticFamily
V [auth U]IPR046755V-type proton ATPase subunit S1, luminal domainDomain
V [auth U]IPR008388V0 complex accessory subunit Ac45Family
V [auth U]IPR046756V-type proton ATPase subunit S1/VOA1, transmembrane domainDomain
W [auth V]IPR056780Renin receptor-like, C-terminal transmembrane spanning segmentDomain
W [auth V]IPR012493Renin receptor-likeFamily
W [auth V]IPR057318Renin receptor, N-terminal domainDomain
X [auth 0]IPR035921F/V-ATP synthase subunit C superfamilyHomologous Superfamily
X [auth 0]IPR002379V-ATPase proteolipid subunit C-like domainDomain
X [auth 0]IPR000245V-ATPase proteolipid subunitFamily
IPR011555V-ATPase proteolipid subunit C, eukaryoticFamily
IPR035921F/V-ATP synthase subunit C superfamilyHomologous Superfamily
IPR002379V-ATPase proteolipid subunit C-like domainDomain
IPR000245V-ATPase proteolipid subunitFamily
HA [auth Q]IPR044911V-type ATP synthase C/D subunit, domain 3 superfamilyHomologous Superfamily
HA [auth Q]IPR036079V-type ATP synthase subunit C/D subunit superfamilyHomologous Superfamily
HA [auth Q]IPR035067V-type ATPase subunit C/DHomologous Superfamily
HA [auth Q]IPR002843ATPase, V0 complex, C/D subunitFamily
HA [auth Q]IPR016727ATPase, V0 complex, subunit DFamily
IA [auth P]IPR004908ATPase, V1 complex, subunit HFamily
IA [auth P]IPR016024Armadillo-type foldHomologous Superfamily
IA [auth P]IPR011989Armadillo-like helicalHomologous Superfamily
IA [auth P]IPR038497ATPase, V1 complex, subunit H, C-terminal domain superfamilyHomologous Superfamily
IA [auth P]IPR011987ATPase, V1 complex, subunit H, C-terminalDomain

Pharos: Disease Associations Pharos Homepage Annotation

ChainsDrug Target  Associated Disease
A [auth R]PharosQ93050
B [auth O]PharosP21283
C [auth J],
E [auth I],
G [auth H]
PharosP36543
D [auth M],
F [auth L],
H [auth K]
PharosO75348
I [auth S]PharosO15342
K [auth B],
L [auth C],
M [auth A]
PharosP38606
N [auth E],
O [auth F],
P [auth D]
PharosP21281
T [auth G]PharosQ9Y5K8
U [auth N]PharosQ16864
V [auth U]PharosQ15904
W [auth V]PharosO75787
X [auth 0]PharosQ99437
HA [auth Q]PharosP61421
IA [auth P]PharosQ9UI12