AiPD: Autoinhibited Protein Database

Q9Y5K8

Gene name	ATP6V1D (ATP6M, VATD)
Protein name	V-type proton ATPase subunit D
Names	V-ATPase subunit D, V-ATPase 28 kDa accessory protein, Vacuolar proton pump subunit D
Species	Homo sapiens (Human)
KEGG Pathway	hsa:51382
EC number
Protein Class

Descriptions

The autoinhibited protein was predicted that may have potential autoinhibitory elements via cis-regPred.

Autoinhibitory domains (AIDs)

79-150 (Predicted disordered autoinhibitory region) PR

Target domain
Relief mechanism
Assay	cis-regPred

AID

79-150 (Predicted disordered autoinhibitory region)

Target domain

Relief mechanism

Assay

cis-regPred

Accessory elements

No accessory elements

References

Yeon JH et al. (2016) "Systems-wide Identification of cis-Regulatory Elements in Proteins", Cell Systems, 2, 89-100

Autoinhibited structure

Activated structure

7 structures for Q9Y5K8

Entry ID	Method	Resolution	Chain	Position	Source
6WLZ	EM	290 A	G	1-247	PDB
6WM2	EM	310 A	G	1-247	PDB
6WM3	EM	340 A	G	1-247	PDB
6WM4	EM	360 A	G	1-247	PDB
7U4T	EM	360 A	G	1-247	PDB
7UNF	EM	408 A	D	1-247	PDB
AF-Q9Y5K8-F1	Predicted				AlphaFoldDB

160 variants for Q9Y5K8

Variant ID(s)	Position	Change	Description	Diseaes Association	Provenance
CA7235472 rs750494530	3	G>C		No	ClinGen ExAC gnomAD
TCGA novel	3	G>D	Variant assessed as Somatic; impact. [NCI-TCGA]	No	NCI-TCGA
rs1363034517 CA390132008	4	K>E		No	ClinGen gnomAD
rs1363034517 CA390132009	4	K>Q		No	ClinGen gnomAD
TCGA novel	5	D>E	Variant assessed as Somatic; impact. [NCI-TCGA]	No	NCI-TCGA
rs765234254 COSM3386641 CA7235471	6	R>*	pancreas [Cosmic]	No	ClinGen cosmic curated ExAC gnomAD
rs1441024453 CA390131976	6	R>Q	Variant assessed as Somatic; 4.632e-05 impact. [NCI-TCGA]	No	ClinGen NCI-TCGA gnomAD
rs972002829 CA262751997	7	I>T		No	ClinGen gnomAD
CA390131971 rs1296128167 COSM93918	7	I>V	lung [Cosmic]	No	ClinGen cosmic curated TOPMed gnomAD
rs1291458422 CA390131953	8	E>A		No	ClinGen TOPMed gnomAD
rs1291458422 CA390131951	8	E>G		No	ClinGen TOPMed gnomAD
CA262751995 rs960972603	9	I>M		No	ClinGen TOPMed gnomAD
rs1310258347 CA390131944 COSM3667664	9	I>V	liver [Cosmic]	No	ClinGen cosmic curated TOPMed
rs754025532 CA7235469	11	P>L	Variant assessed as Somatic; 0.0 impact. [NCI-TCGA]	No	ClinGen ExAC NCI-TCGA gnomAD
rs1382452548 CA390131917	11	P>S	Variant assessed as Somatic; impact. [NCI-TCGA]	No	ClinGen NCI-TCGA TOPMed gnomAD
TCGA novel	12	S>R	Variant assessed as Somatic; impact. [NCI-TCGA]	No	NCI-TCGA
CA390131885 rs1432163079	13	R>Q		No	ClinGen gnomAD
CA7235448 rs756466933	16	Q>*		No	ClinGen ExAC gnomAD
rs1195889684 CA390130343	17	T>S		No	ClinGen gnomAD
CA7235446 rs373531466	21	A>P		No	ClinGen ESP ExAC TOPMed gnomAD
CA262747306 rs373531466	21	A>S		No	ClinGen ESP ExAC TOPMed gnomAD
rs142143626 CA262747295	22	R>C		No	ClinGen ESP ExAC gnomAD
CA7235443 rs145144886	22	R>H		No	ClinGen ESP ExAC TOPMed gnomAD
CA7235444 rs145144886	22	R>P		No	ClinGen ESP ExAC TOPMed gnomAD
rs142143626 CA7235445	22	R>S		No	ClinGen ESP ExAC gnomAD
TCGA novel	24	K>R	Variant assessed as Somatic; impact. [NCI-TCGA]	No	NCI-TCGA
CA7235442 rs761204674	26	A>V		No	ClinGen ExAC TOPMed gnomAD
rs369382914 CA7235441	27	Q>H		No	ClinGen ESP ExAC TOPMed gnomAD
rs1364562185 CA390130277	27	Q>L		No	ClinGen gnomAD
CA7235439 rs760322362	28	T>A		No	ClinGen ExAC gnomAD
rs760322362 CA7235440	28	T>S		No	ClinGen ExAC gnomAD
TCGA novel	29	G>S	Variant assessed as Somatic; impact. [NCI-TCGA]	No	NCI-TCGA
rs771874211 CA390130265	30	R>*		No	ClinGen ExAC TOPMed gnomAD
rs771874211 CA7235437	30	R>G		No	ClinGen ExAC TOPMed gnomAD
CA7235435 rs772067354	30	R>L		No	ClinGen ExAC TOPMed gnomAD
COSM957162 rs772067354 CA7235436	30	R>Q	Variant assessed as Somatic; 0.0 impact. liver endometrium [NCI-TCGA, Cosmic]	No	ClinGen cosmic curated ExAC NCI-TCGA TOPMed gnomAD
CA390130248 rs1425415596	33	L>M		No	ClinGen TOPMed gnomAD
CA390130249 rs1425415596	33	L>V		No	ClinGen TOPMed gnomAD
CA390130237 rs1199338491	34	K>N		No	ClinGen gnomAD
CA390130240 rs1254010789	34	K>R		No	ClinGen gnomAD
rs770953326 CA7235434	37	S>C		No	ClinGen ExAC gnomAD
rs1281954651	37	S>I	Variant assessed as Somatic; 0.0 impact. [NCI-TCGA]	No	NCI-TCGA
CA262747239 rs139045883	38	D>V		No	ClinGen ESP
CA7235433 rs749319649	41	T>A		No	ClinGen ExAC TOPMed gnomAD
CA390130194 rs749319649	41	T>S		No	ClinGen ExAC TOPMed gnomAD
CA7235432 rs777979181	42	L>F		No	ClinGen ExAC TOPMed gnomAD
rs150707025 CA7235431	43	R>*		No	ClinGen ESP ExAC TOPMed gnomAD
rs749286842 CA7235430	45	R>*	Variant assessed as Somatic; 0.0 impact. [NCI-TCGA]	No	ClinGen ExAC NCI-TCGA TOPMed gnomAD
rs781650138 CA390130172	45	R>L		No	ClinGen ExAC TOPMed gnomAD
rs781650138 CA7235429	45	R>Q	Variant assessed as Somatic; 0.0 impact. [NCI-TCGA]	No	ClinGen ExAC NCI-TCGA TOPMed gnomAD
TCGA novel	49	K>N	Variant assessed as Somatic; impact. [NCI-TCGA]	No	NCI-TCGA
CA390130150 rs1396003503	49	K>Q		No	ClinGen gnomAD
CA7235426 rs766781389	52	I>M		No	ClinGen ExAC gnomAD
rs1322709447 CA390130118	53	E>A		No	ClinGen gnomAD
TCGA novel	53	E>Q	Variant assessed as Somatic; impact. [NCI-TCGA]	No	NCI-TCGA
rs758770521 CA7235407	54	T>N		No	ClinGen ExAC TOPMed gnomAD
rs763552551 CA7235405	56	M>V		No	ClinGen ExAC gnomAD
CA7235404 rs142126455	57	L>M		No	ClinGen ESP ExAC TOPMed gnomAD
CA390129499 rs1265699471	58	M>T		No	ClinGen gnomAD
rs767146743 CA390129486	60	E>K	Variant assessed as Somatic; 0.0 impact. [NCI-TCGA]	No	ClinGen ExAC NCI-TCGA TOPMed gnomAD
rs767146743 CA7235402	60	E>Q		No	ClinGen ExAC TOPMed gnomAD
CA390129461 rs1277423284	61	V>G		No	ClinGen gnomAD
rs759303675 CA7235401	64	E>D		No	ClinGen ExAC
TCGA novel	68	S>Y	Variant assessed as Somatic; impact. [NCI-TCGA]	No	NCI-TCGA
CA262745908 rs957536902	70	A>V		No	ClinGen TOPMed
TCGA novel	72	A>V	Variant assessed as Somatic; impact. [NCI-TCGA]	No	NCI-TCGA
rs1412279405 CA390129084	81	T>A		No	ClinGen gnomAD
rs372372939 CA390129025	85	Q>H		No	ClinGen ESP ExAC TOPMed gnomAD
TCGA novel	87	V>A	Variant assessed as Somatic; impact. [NCI-TCGA]	No	NCI-TCGA
rs17852866 CA262744922	88	N>H		No	ClinGen Ensembl
CA7235383 rs767024105	88	N>S		No	ClinGen ExAC TOPMed gnomAD
CA7235382 rs754532623	90	A>V	Variant assessed as Somatic; 0.0 impact. [NCI-TCGA]	No	ClinGen ExAC NCI-TCGA gnomAD
CA390128967 rs1472518450	93	K>N		No	ClinGen gnomAD
rs1466502599 CA390128964	94	I>F		No	ClinGen TOPMed
rs766049551 CA390128959	95	R>*		No	ClinGen ExAC TOPMed gnomAD
CA7235380 rs766049551	95	R>G		No	ClinGen ExAC TOPMed gnomAD
CA7235379 rs762779445	95	R>Q		No	ClinGen ExAC TOPMed gnomAD
CA390128956 rs1278068027	96	A>T		No	ClinGen gnomAD
CA7235378 rs773197310	96	A>V	Variant assessed as Somatic; 0.0 impact. [NCI-TCGA]	No	ClinGen ExAC NCI-TCGA TOPMed gnomAD
CA7235331 rs774643510	106	L>F		No	ClinGen ExAC TOPMed gnomAD
CA390128848 rs1186124178	110	E>A		No	ClinGen gnomAD
CA7235329 rs771311974	113	H>R		No	ClinGen ExAC gnomAD
rs749755181 CA7235328	114	E>Q		No	ClinGen ExAC gnomAD
CA390137907 rs1463498660	120	E>K		No	ClinGen gnomAD
TCGA novel	122	T>I	Variant assessed as Somatic; impact. [NCI-TCGA]	No	NCI-TCGA
rs1202033549 CA390137733	139	A>T		No	ClinGen TOPMed
CA7235308 rs771183488	140	K>E		No	ClinGen ExAC TOPMed gnomAD
TCGA novel	142	V>D	Variant assessed as Somatic; impact. [NCI-TCGA]	No	NCI-TCGA
CA390137693 rs1289431347	142	V>M		No	ClinGen gnomAD
rs201955108 CA262778452	144	L>V		No	ClinGen Ensembl
CA7235305 rs770266758	147	E>A		No	ClinGen ExAC gnomAD
CA390137600 rs1164621637	148	L>V		No	ClinGen gnomAD
rs748614540 CA7235304	150	S>C		No	ClinGen ExAC gnomAD
CA390137556 rs748614540	150	S>F		No	ClinGen ExAC gnomAD
rs558520021 CA7235302	151	L>R		No	ClinGen 1000Genomes ExAC gnomAD
TCGA novel CA7235301 rs745407370	152	Q>H	Variant assessed as Somatic; impact. [NCI-TCGA]	No	NCI-TCGA ClinGen ExAC TOPMed gnomAD
CA390137533 rs1410586772	152	Q>L		No	ClinGen TOPMed
rs1425545110 CA390137287	153	T>I		No	ClinGen TOPMed gnomAD
CA262777030 COSM3815144 rs941409496	154	S>C	Variant assessed as Somatic; impact. breast [NCI-TCGA, Cosmic]	No	ClinGen cosmic curated Ensembl NCI-TCGA
rs765541892 CA7235288	159	D>H		No	ClinGen ExAC gnomAD
CA7235287 rs138958323	164	I>V		No	ClinGen ESP ExAC TOPMed gnomAD
CA390137073 rs1348959179	165	T>I		No	ClinGen gnomAD
CA262777008 rs761280664	166	N>S		No	ClinGen gnomAD
rs776968392 CA7235286	167	R>M	Variant assessed as Somatic; 0.0 impact. [NCI-TCGA]	No	ClinGen ExAC NCI-TCGA gnomAD
CA390137036 rs1366148258	168	R>C		No	ClinGen gnomAD
TCGA novel	171	A>V	Variant assessed as Somatic; impact. [NCI-TCGA]	No	NCI-TCGA
rs971378799 CA262776972	174	H>L		No	ClinGen TOPMed
CA390136921 rs1383952735	175	V>F		No	ClinGen gnomAD
CA390136923 rs1383952735	175	V>I		No	ClinGen gnomAD
rs772713686 CA7235254	176	I>V		No	ClinGen ExAC gnomAD
CA7235253 rs376721505	177	I>V		No	ClinGen ESP ExAC TOPMed gnomAD
rs866817285 CA262774901	178	P>S		No	ClinGen Ensembl
rs144396308 CA7235251 COSM143400	179	R>Q	upper_aerodigestive_tract [Cosmic]	No	ClinGen cosmic curated ESP ExAC TOPMed gnomAD
CA7235252 rs747884101	179	R>W		No	ClinGen ExAC gnomAD
rs1268500943 CA390135958	180	I>M		No	ClinGen Ensembl
CA262774879 rs993708581	180	I>V		No	ClinGen TOPMed
CA7235248 rs149627999	182	R>C		No	ClinGen 1000Genomes ESP ExAC TOPMed gnomAD
CA7235247 rs780067544	182	R>H		No	ClinGen ExAC TOPMed gnomAD
rs780067544 CA390135926	182	R>L		No	ClinGen ExAC TOPMed gnomAD
rs758377727 CA7235246	183	T>S		No	ClinGen ExAC gnomAD
CA7235244 rs369607221	185	A>V		No	ClinGen ESP ExAC gnomAD
CA7235243 rs757563160	186	Y>*		No	ClinGen ExAC gnomAD
CA390135798 rs1402352566	188	I>T		No	ClinGen gnomAD
CA7235240 rs761217080	192	D>H		No	ClinGen ExAC gnomAD
rs753288296 CA7235239	193	E>G		No	ClinGen ExAC gnomAD
CA7235238 rs201968492	194	R>S		No	ClinGen 1000Genomes ExAC TOPMed gnomAD
rs1179702514 CA390135656	195	E>A		No	ClinGen gnomAD
CA7235237 rs762351423	196	R>*		No	ClinGen ExAC
rs772839739 CA390135564	200	Y>C		No	ClinGen ExAC TOPMed gnomAD
CA7235235 rs772839739	200	Y>F		No	ClinGen ExAC TOPMed gnomAD
CA262773753 rs200296816	204	K>R		No	ClinGen 1000Genomes
CA7235218 rs564093655	205	I>L		No	ClinGen 1000Genomes ExAC TOPMed gnomAD
CA390135004 rs1356967224	205	I>M		No	ClinGen gnomAD
CA390135010 rs1223138203	205	I>T		No	ClinGen gnomAD
rs767901235 CA7235217	209	K>E		No	ClinGen ExAC
rs1449859980 CA390134871	214	E>Q		No	ClinGen gnomAD
CA262773752 rs868002281	216	S>A		No	ClinGen Ensembl
rs1381534513 CA390134834	216	S>Y		No	ClinGen gnomAD
rs760159563 CA7235216	217	E>A		No	ClinGen ExAC gnomAD
rs760159563 CA390134818	217	E>G		No	ClinGen ExAC gnomAD
CA7235215 rs749838978	218	K>E		No	ClinGen ExAC gnomAD
CA7235214 CA390134793 rs764819379	219	D>E		No	ClinGen ExAC TOPMed gnomAD
CA262773717 rs953247463	225	A>T		No	ClinGen Ensembl
CA262773711 rs921865135	225	A>V		No	ClinGen Ensembl
rs572349725 CA262773707	227	G>R		No	ClinGen gnomAD
rs776231135 CA7235212	228	E>D		No	ClinGen ExAC TOPMed gnomAD
CA7235211 rs527374469	229	V>M		No	ClinGen 1000Genomes ExAC gnomAD
CA7235209 rs775421239	232	P>L		No	ClinGen ExAC gnomAD
CA262773657 rs150392973	232	P>S		No	ClinGen ESP TOPMed gnomAD
CA390134626 rs1170137678	233	A>P		No	ClinGen TOPMed
rs1240074181 CA390134612	234	N>H		No	ClinGen gnomAD
rs771836108 CA7235208	239	E>D		No	ClinGen ExAC
rs745829564 CA7235207	240	K>*		No	ClinGen ExAC
rs1352998389 CA390134526	240	K>N		No	ClinGen TOPMed
CA390134516 rs1463666599	241	D>G		No	ClinGen TOPMed
TCGA novel	242	E>D	Variant assessed as Somatic; impact. [NCI-TCGA]	No	NCI-TCGA
rs771168394 CA7235204 COSM73779	242	E>K	ovary Variant assessed as Somatic; 0.0 impact. large_intestine [Cosmic, NCI-TCGA]	No	ClinGen cosmic curated ExAC NCI-TCGA TOPMed gnomAD
CA390134462 rs1403085606	245	L>R		No	ClinGen TOPMed
CA7235202 rs778118893	246	F>S		No	ClinGen ExAC gnomAD
rs756467063 CA7235201	248	E>Q		No	ClinGen ExAC gnomAD

No associated diseases with Q9Y5K8

3 regional properties for Q9Y5K8

Type	Name	Position	InterPro Accession
domain	ATPase, F1/V1/A1 complex, alpha/beta subunit, nucleotide-binding domain	173 - 399	IPR000194
domain	ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain	50 - 116	IPR004100
active_site	ATPase, alpha/beta subunit, nucleotide-binding domain, active site	390 - 399	IPR020003

Functions

		Description
EC Number
Subcellular Localization	Membrane ; Peripheral membrane protein ; Cytoplasmic side Cytoplasmic vesicle, clathrin-coated vesicle membrane ; Peripheral membrane protein Cytoplasm, cytoskeleton, microtubule organizing center, centrosome Cell projection, cilium	Localizes to centrosome and the base of the cilium
PANTHER Family
PANTHER Subfamily
PANTHER Protein Class
PANTHER Pathway Category	No pathway information available

13 GO annotations of cellular component

Name	Definition
cilium	A specialized eukaryotic organelle that consists of a filiform extrusion of the cell surface and of some cytoplasmic parts. Each cilium is largely bounded by an extrusion of the cytoplasmic (plasma) membrane, and contains a regular longitudinal array of microtubules, anchored to a basal body.
clathrin-coated vesicle membrane	The lipid bilayer surrounding a clathrin-coated vesicle.
cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
endosome membrane	The lipid bilayer surrounding an endosome.
extracellular exosome	A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
Golgi membrane	The lipid bilayer surrounding any of the compartments of the Golgi apparatus.
lysosomal membrane	The lipid bilayer surrounding the lysosome and separating its contents from the cell cytoplasm.
membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
microtubule organizing center	An intracellular structure that can catalyze gamma-tubulin-dependent microtubule nucleation and that can anchor microtubules by interacting with their minus ends, plus ends or sides.
plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
proton-transporting V-type ATPase complex	A proton-transporting two-sector ATPase complex that couples ATP hydrolysis to the transport of protons across a concentration gradient. The resulting transmembrane electrochemical potential of H+ is used to drive a variety of (i) secondary active transport systems via H+-dependent symporters and antiporters and (ii) channel-mediated transport systems. The complex comprises a membrane sector (V0) that carries out proton transport and a cytoplasmic compartment sector (V1) that catalyzes ATP hydrolysis. V-type ATPases are found in the membranes of organelles such as vacuoles, endosomes, and lysosomes, and in the plasma membrane.
specific granule membrane	The lipid bilayer surrounding a specific granule, a granule with a membranous, tubular internal structure, found primarily in mature neutrophil cells. Most are released into the extracellular fluid. Specific granules contain lactoferrin, lysozyme, vitamin B12 binding protein and elastase.
vacuolar proton-transporting V-type ATPase, V1 domain	The V1 domain of a proton-transporting V-type ATPase found in the vacuolar membrane.

1 GO annotations of molecular function

Name	Definition
proton-transporting ATPase activity, rotational mechanism	Enables the transfer of protons from one side of a membrane to the other according to the reaction: ATP + H2O + H+(in) = ADP + phosphate + H+(out), by a rotational mechanism.

9 GO annotations of biological process

Name	Definition
cilium assembly	The assembly of a cilium, a specialized eukaryotic organelle that consists of a filiform extrusion of the cell surface. Each cilium is bounded by an extrusion of the cytoplasmic membrane, and contains a regular longitudinal array of microtubules, anchored basally in a centriole.
endosomal lumen acidification	Any process that reduces the pH of the endosomal lumen, measured by the concentration of the hydrogen ion.
Golgi lumen acidification	Any process that reduces the pH of the Golgi lumen, measured by the concentration of the hydrogen ion.
intracellular pH reduction	Any process that reduces the internal pH of a cell, measured by the concentration of the hydrogen ion.
lysosomal lumen acidification	Any process that reduces the pH of the lysosomal lumen, measured by the concentration of the hydrogen ion.
protein localization to cilium	A process in which a protein is transported to, or maintained in, a location within a cilium.
proton transmembrane transport	The directed movement of a proton across a membrane.
regulation of macroautophagy	Any process that modulates the frequency, rate or extent of macroautophagy.
vacuolar acidification	Any process that reduces the pH of the vacuole, measured by the concentration of the hydrogen ion.

4 homologous proteins in AiPD

UniProt AC	Gene Name	Protein Name	Species	Evidence Code
P32610	VMA8	V-type proton ATPase subunit D	Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)	PR
P39942	ATP6V1D	V-type proton ATPase subunit D	Bos taurus (Bovine)	PR
Q9V7D2	Vha36-1	V-type proton ATPase subunit D 1	Drosophila melanogaster (Fruit fly)	PR
P57746	Atp6v1d	V-type proton ATPase subunit D	Mus musculus (Mouse)	PR

10	20	30	40	50	60
MSGKDRIEIF	PSRMAQTIMK	ARLKGAQTGR	NLLKKKSDAL	TLRFRQILKK	IIETKMLMGE
70	80	90	100	110	120
VMREAAFSLA	EAKFTAGDFS	TTVIQNVNKA	QVKIRAKKDN	VAGVTLPVFE	HYHEGTDSYE
130	140	150	160	170	180
LTGLARGGEQ	LAKLKRNYAK	AVELLVELAS	LQTSFVTLDE	AIKITNRRVN	AIEHVIIPRI
190	200	210	220	230	240
ERTLAYIITE	LDEREREEFY	RLKKIQEKKK	ILKEKSEKDL	EQRRAAGEVL	EPANLLAEEK

DEDLLFE