3J9V: Yeast V-ATPase state 3

Yeast V-ATPase state 3. Determined by electron microscopy at 8.3 Å resolution. Released 13 May 2015.

Method: Electron microscopy
Resolution: 8.3 Å
Organism: Saccharomyces cerevisiae
Chains: 28
Atoms: 57,659
Mol. weight: 934.64 kDa
Released: 13 May 2015

Explore 3J9V in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3J9V contains 297 α-helices and 215 β-strands across 28 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain a: 6 helices, 0 β-strands

Element	Residues	Length
α-helix	13-43	31
α-helix	50-77	28
α-helix	84-121	38
α-helix	123-125	3
α-helix	126-134	9
α-helix	137-154	18

Chain A: 27 helices, 31 β-strands

Element	Residues	Length	Sheet
β-strand	25-31	7	10
β-strand	34-38	5	10
β-strand	47-51	5	10
β-strand	56-64	9	10
β-strand	67-72	6	10
α-helix	79	1
β-strand	80	1	24
β-strand	84-91	8	10
β-strand	94-96	3	25
β-strand	104-105	2	26
β-strand	111	1	26
α-helix	112-119	8
α-helix	124-125	2
β-strand	138-141	4	27
β-strand	142-143	2	28
β-strand	151-152	2	29
β-strand	157-160	4	28
β-strand	171-173	3	28
α-helix	174-175	2
β-strand	180-185	6	29
α-helix	186-187	2
β-strand	189-192	4	27
β-strand	196-202	7	29
β-strand	204-210	7	29
β-strand	213-215	3	25
β-strand	225-226	2	26
β-strand	231	1	30
α-helix	238-243	6
β-strand	248	1	30
β-strand	251-254	4	26
α-helix	262-272	11
β-strand	277-285	9	26
α-helix	288-296	9
α-helix	297-299	3
α-helix	301-302	2
α-helix	310-313	4
β-strand	315-321	7	26
α-helix	326-346	21
β-strand	349-355	7	26
α-helix	357-371	15
α-helix	384-394	11
β-strand	396-399	4	26
α-helix	400	1
β-strand	407-415	9	26
α-helix	426-434	9
β-strand	437-438	2	26
α-helix	443-449	7
α-helix	451	1
α-helix	453	1
β-strand	460-461	2	26
α-helix	464-474	11
α-helix	478-501	24
α-helix	509-521	13
α-helix	522-526	5
α-helix	540-562	23
α-helix	567-582	16
α-helix	584-586	3
α-helix	598-615	18

Chain b: 9 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	15-21	7	1
α-helix	26-34	9
β-strand	39-43	5	1
α-helix	56-79	24
α-helix	94-99	6
α-helix	107-150	44
β-strand	185-191	7	2
α-helix	194-208	15
β-strand	213-218	6	2
β-strand	235-241	7	2
α-helix	246-256	11
β-strand	261	1	2
α-helix	273-323	51
α-helix	327-330	4
β-strand	335-341	7	1
α-helix	346-351	6
β-strand	360-361	2	1

Chain B: 16 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	31-35	5	10
β-strand	38-41	4	10
β-strand	48	1	24
β-strand	51-56	6	10
β-strand	62-71	10	10
β-strand	74-79	6	10
β-strand	92-99	8	10
β-strand	101-104	4	31
β-strand	111-114	4	32
β-strand	130-133	4	31
β-strand	150	1	33
α-helix	156-159	4
β-strand	165	1	33
β-strand	169	1	32
β-strand	172-175	4	34
α-helix	180-190	11
α-helix	194-201	8
β-strand	208-214	7	32
α-helix	219-232	14
β-strand	238-242	5	32
α-helix	249-269	21
β-strand	273-278	6	32
α-helix	281-290	10
α-helix	301-303	3
α-helix	308-317	10
β-strand	320-321	2	32
α-helix	322	1
β-strand	328-333	6	32
β-strand	334-337	4	34
α-helix	345-353	9
β-strand	356-360	5	34
α-helix	362-367	6
β-strand	373-380	8	34
α-helix	383-386	4
α-helix	396-419	24
α-helix	427-440	14
α-helix	454-465	12
α-helix	478-483	6

Chain C: 23 helices, 34 β-strands

Element	Residues	Length	Sheet
β-strand	26-31	6	10
β-strand	34-38	5	10
β-strand	47-51	5	10
β-strand	56-64	9	10
β-strand	67-72	6	10
α-helix	79-80	2
β-strand	85-91	7	10
β-strand	93-96	4	35
β-strand	104-105	2	36
β-strand	111	1	36
α-helix	112-119	8
β-strand	138-141	4	37
β-strand	142-143	2	38
β-strand	151-153	3	39
β-strand	157-161	5	38
β-strand	170-173	4	38
α-helix	174-175	2
β-strand	179-185	7	39
β-strand	189-192	4	37
β-strand	196-201	6	39
β-strand	205-210	6	39
β-strand	213-216	4	35
α-helix	220-222	3
β-strand	225-227	3	36
β-strand	232-233	2	40
α-helix	238-243	6
β-strand	246-247	2	40
β-strand	252-255	4	36
α-helix	262-272	11
β-strand	277-282	6	36
β-strand	285	1	41
α-helix	288-296	9
α-helix	310-313	4
β-strand	315-318	4	36
β-strand	321	1	41
α-helix	326-346	21
β-strand	349-355	7	36
α-helix	358-371	14
α-helix	377-379	3
α-helix	383-393	11
β-strand	396-399	4	36
β-strand	407-416	10	36
α-helix	426-434	9
β-strand	437-439	3	36
α-helix	443-447	5
α-helix	456-458	3
β-strand	459-461	3	36
α-helix	464-474	11
α-helix	478-501	24
α-helix	509-526	18
α-helix	540-562	23
α-helix	567-574	8
α-helix	576-582	7
α-helix	583-585	3
β-strand	592	1	42
β-strand	596	1	42
α-helix	598-615	18

Chain D: 16 helices, 27 β-strands

Element	Residues	Length	Sheet
β-strand	31-35	5	10
β-strand	38-41	4	10
α-helix	48	1
β-strand	51-56	6	10
β-strand	62-71	10	10
β-strand	74-79	6	10
β-strand	92-99	8	10
β-strand	101-104	4	43
β-strand	111-114	4	44
β-strand	119	1	44
β-strand	130-133	4	43
β-strand	150	1	45
α-helix	156-159	4
β-strand	165	1	45
β-strand	169	1	44
β-strand	172-174	3	46
α-helix	180-190	11
α-helix	195-201	7
β-strand	208-214	7	44
α-helix	219-232	14
β-strand	238-242	5	44
α-helix	249-269	21
β-strand	273-279	7	44
α-helix	281-293	13
β-strand	299	1	47
α-helix	301-303	3
β-strand	305	1	47
α-helix	308-317	10
β-strand	320-322	3	44
β-strand	327-333	7	44
β-strand	334-336	3	46
α-helix	345-353	9
β-strand	357	1	48
β-strand	358-359	2	46
β-strand	360	1	49
α-helix	362-367	6
β-strand	373	1	49
β-strand	379	1	48
α-helix	396-420	25
α-helix	427-438	12
α-helix	439-443	5
α-helix	454-465	12
α-helix	478-483	6

Chain E: 24 helices, 32 β-strands

Element	Residues	Length	Sheet
β-strand	25-31	7	10
β-strand	34-38	5	10
β-strand	47-51	5	10
β-strand	56-64	9	10
β-strand	67-72	6	10
β-strand	80	1	11
β-strand	84-91	8	10
β-strand	93-96	4	12
β-strand	104-105	2	13
β-strand	111	1	13
α-helix	112-118	7
α-helix	124-125	2
β-strand	138-143	6	14
β-strand	151-152	2	15
β-strand	157-162	6	14
β-strand	168-173	6	14
α-helix	174-175	2
β-strand	180-185	6	15
α-helix	186-187	2
β-strand	189-192	4	14
β-strand	198-201	4	15
β-strand	205-209	5	15
β-strand	213-216	4	12
α-helix	220-222	3
β-strand	223-227	5	13
α-helix	238-243	6
β-strand	251-255	5	13
α-helix	262-272	11
β-strand	277-285	9	13
α-helix	288-299	12
α-helix	310-314	5
β-strand	315-321	7	13
α-helix	326-346	21
β-strand	349-355	7	13
α-helix	357-371	15
α-helix	373-375	3
α-helix	377-379	3
α-helix	384-394	11
β-strand	397-400	4	13
β-strand	407-416	10	13
β-strand	419	1	16
β-strand	422	1	16
α-helix	426-434	9
β-strand	437-439	3	13
α-helix	443-448	6
β-strand	450	1	17
β-strand	459-461	3	13
α-helix	464-474	11
α-helix	478-501	24
α-helix	509-521	13
α-helix	522-526	5
β-strand	527	1	17
α-helix	540-564	25
α-helix	567-582	16
α-helix	583-585	3
α-helix	598-615	18

Chain F: 17 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	31-35	5	10
β-strand	38-41	4	10
β-strand	48	1	11
β-strand	51-56	6	10
β-strand	62-71	10	10
β-strand	74-79	6	10
β-strand	92-99	8	10
β-strand	101-104	4	18
β-strand	112-114	3	19
β-strand	119	1	19
β-strand	130-133	4	18
β-strand	150-151	2	20
α-helix	156-162	7
β-strand	164-165	2	20
β-strand	169	1	19
β-strand	172-175	4	21
α-helix	180-190	11
α-helix	194-201	8
β-strand	208-217	10	19
α-helix	219-232	14
β-strand	238-244	7	19
α-helix	249-269	21
β-strand	273-279	7	19
α-helix	281-290	10
α-helix	298-299	2
α-helix	301-303	3
α-helix	308-317	10
β-strand	320-322	3	19
β-strand	327-333	7	19
β-strand	334-337	4	21
α-helix	345-353	9
β-strand	356-357	2	22
β-strand	358-359	2	21
β-strand	360	1	23
α-helix	362-367	6
β-strand	373	1	23
β-strand	379-380	2	22
α-helix	395-420	26
α-helix	427-438	12
α-helix	439-443	5
α-helix	454-465	12
α-helix	470-472	3
α-helix	478-483	6

20 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
V-type proton ATPase subunit a, vacuolar isoform	b	protein	840	Saccharomyces cerevisiae	P32563 (AlphaFold model)
V-type proton ATPase subunit C	O	protein	392	Saccharomyces cerevisiae	P31412 (AlphaFold model)
V-type proton ATPase subunit D	M	protein	256	Saccharomyces cerevisiae	P32610 (AlphaFold model)
V-type proton ATPase subunit F	N	protein	118	Saccharomyces cerevisiae	P39111 (AlphaFold model)
V-type proton ATPase catalytic subunit A	A, C, E	protein	616	Saccharomyces cerevisiae	P17255
V-type proton ATPase subunit B	B, D, F	protein	517	Saccharomyces cerevisiae	P16140
V-type proton ATPase subunit d	Q	protein	345	Saccharomyces cerevisiae	P32366
V-type proton ATPase subunit G	H, J, L	protein	114	Saccharomyces cerevisiae	P48836
V-type proton ATPase subunit E	G, I, K	protein	233	Saccharomyces cerevisiae	P22203
V-type proton ATPase subunit H	P	protein	478	Saccharomyces cerevisiae	P41807
V-type proton ATPase subunit c	R, S, T, U, V, W, X, Y, Z, a	protein	160	Saccharomyces cerevisiae	P25515

Sequence of entity 1 (b), FASTA

>3J9V_1 V-type proton ATPase subunit a, vacuolar isoform (chains b)
MAEKEEAIFRSAEMALVQFYIPQEISRDSAYTLGQLGLVQFRDLNSKVRAFQRTFVNEIR
RLDNVERQYRYFYSLLKKHDIKLYEGDTDKYLDGSGELYVPPSGSVIDDYVRNASYLEER
LIQMEDATDQIEVQKNDLEQYRFILQSGDEFFLKGDNTDSTSYMDEDMIDANGENIAAAI
GASVNYVTGVIARDKVATLEQILWRVLRGNLFFKTVEIEQPVYDVKTREYKHKNAFIVFS
HGDLIIKRIRKIAESLDANLYDVDSSNEGRSQQLAKVNKNLSDLYTVLKTTSTTLESELY
AIAKELDSWFQDVTREKAIFEILNKSNYDTNRKILIAEGWIPRDELATLQARLGEMIARL
GIDVPSIIQVLDTNHTPPTFHRTNKFTAGFQSICDCYGIAQYREINAGLPTIVTFPFMFA
IMFGDMGHGFLMTLAALSLVLNEKKINKMKRGEIFDMAFTGRYIILLMGVFSMYTGFLYN
DIFSKTMTIFKSGWKWPDHWKKGESITATSVGTYPIGLDWAWHGTENALLFSNSYKMKLS
ILMGFIHMTYSYFFSLANHLYFNSMIDIIGNFIPGLLFMQGIFGYLSVCIVYKWAVDWVK
DGKPAPGLLNMLINMFLSPGTIDDELYPHQAKVQVFLLLMALVCIPWLLLVKPLHFKFTH
KKKSHEPLPSTEADASSEDLEAQQLISAMDADDAEEEEVGSGSHGEDFGDIMIHQVIHTI
EFCLNCVSHTASYLRLWALSLAHAQLSSVLWTMTIQIAFGFRGFVGVFMTVALFAMWFAL
TCAVLVLMEGTSAMLHSLRLHWVESMSKFFVGEGLPYEPFAFEYKDMEVAVASASSSASS

Sequence of entity 2 (O), FASTA

>3J9V_2 V-type proton ATPase subunit C (chains O)
MATALYTANDFILISLPQNAQPVTAPGSKTDSWFNETLIGGRAFVSDFKIPEFKIGSLDT
LIVESEELSKVDNQIGASIGKIIEILQGLNETSTNAYRTLPINNMPVPEYLENFQWQTRK
FKLDKSIKDLITLISNESSQLDADVRATYANYNSAKTNLAAAERKKTGDLSVRSLHDIVK
PEDFVLNSEHLTTVLVAVPKSLKSDFEKSYETLSKNVVPASASVIAEDAEYVLFNVHLFK
KNVQEFTTAAREKKFIPREFNYSEELIDQLKKEHDSAASLEQSLRVQLVRLAKTAYVDVF
INWFHIKALRVYVESVLRYGLPPHFNIKIIAVPPKNLSKCKSELIDAFGFLGGNAFMKDK
KGKINKQDTSLHQYASLVDTEYEPFVMYIINL

Sequence of entity 3 (M), FASTA

>3J9V_3 V-type proton ATPase subunit D (chains M)
MSGNREQVFPTRMTLGLMKTKLKGANQGYSLLKRKSEALTKRFRDITKRIDDAKQKMGRV
MQTAAFSLAEVSYATGENIGYQVQESVSTARFKVRARQENVSGVYLSQFESYIDPEINDF
RLTGLGRGGQQVQRAKEIYSRAVETLVELASLQTAFIILDEVIKVTNRRVNAIEHVIIPR
TENTIAYINSELDELDREEFYRLKKVQEKKQNETAKLDAEMKLKRDRAEQDASEVAADEE
PQGETLVADQEDDVIF

Sequence of entity 4 (N), FASTA

>3J9V_4 V-type proton ATPase subunit F (chains N)
MAEKRTLIAVIADEDTTTGLLLAGIGQITPETQEKNFFVYQEGKTTKEEITDKFNHFTEE
RDDIAILLINQHIAENIRARVDSFTNAFPAILEIPSKDHPYDPEKDSVLKRVRKLFGE

Sequence of entity 5 (A, C, E), FASTA

>3J9V_5 V-type proton ATPase catalytic subunit A (chains A, C, E)
AGAIENARKEIKRISLEDHAESEYGAIYSVSGPVVIAENMIGCAMYELVKVGHDNLVGEV
IRIDGDKATIQVYEETAGLTVGDPVLRTGKPLSVELGPGLMETIYDGIQRPLKAIKEESQ
SIYIPRGIDTPALDRTIKWQFTPGKFQVGDHISGGDIYGSVFENSLISSHKILLPPRSRG
TITWIAPAGEYTLDEKILEVEFDGKKSDFTLYHTWPVRVPRPVTEKLSADYPLLTGQRVL
DALFPCVQGGTTCIPGAFGCGKTVISQSLSKYSNSDAIIYVGCGERGNEMAEVLMEFPEL
YTEMSGTKEPIMKRTTLVANTSNMPVAAREASIYTGITLAEYFRDQGKNVSMIADSSSRW
AEALREISGRLGEMPADQGFPAYLGAKLASFYERAGKAVALGSPDRTGSVSIVAAVSPAG
GDFSDPVTTATLGITQVFWGLDKKLAQRKHFPSINTSVSYSKYTNVLNKFYDSNYPEFPV
LRDRMKEILSNAEELEQVVQLVGKSALSDSDKITLDVATLIKEDFLQQNGYSTYDAFCPI
WKTFDMMRAFISYHDEAQKAVANGANWSKLADSTGDVKHAVSSSKFFEPSRGEKEVHGEF
EKLLSTMQERFAESTD

Sequence of entity 6 (B, D, F), FASTA

>3J9V_6 V-type proton ATPase subunit B (chains B, D, F)
MVLSDKELFAINKKAVEQGFNVKPRLNYNTVSGVNGPLVILEKVKFPRYNEIVNLTLPDG
TVRQGQVLEIRGDRAIVQVFEGTSGIDVKKTTVEFTGESLRIPVSEDMLGRIFDGSGRPI
DNGPKVFAEDYLDINGSPINPYARIYPEEMISTGVSAIDTMNSIARGQKIPIFSASGLPH
NEIAAQICRQAGLVRPTKDVHDGHEENFSIVFAAMGVNLETARFFKQDFEENGSLERTSL
FLNLANDPTIERIITPRLALTTAEYLAYQTERHVLTILTDMSSYADALREVSAAREEVPG
RRGYPGYMYTDLSTIYERAGRVEGRNGSITQIPILTMPNDDITHPIPDLTGYITEGQIFV
DRQLHNKGIYPPINVLPSLSRLMKSAIGEGMTRKDHGDVSNQLYAKYAIGKDAAAMKAVV
GEEALSIEDKLSLEFLEKFEKTFITQGAYEDRTVFESLDQAWSLLRIYPKEMLNRISPKI
LDEFYDRARDDADEDEEDPDTRSSGKKKDASQEESLI

Sequence of entity 7 (Q), FASTA

>3J9V_7 V-type proton ATPase subunit d (chains Q)
MEGVYFNIDNGFIEGVVRGYRNGLLSNNQYINLTQCDTLEDLKLQLSSTDYGNFLSSVSS
ESLTTSLIQEYASSKLYHEFNYIRDQSSGSTRKFMDYITYGYMIDNVALMITGTIHDRDK
GEILQRCHPLGWFDTLPTLSVATDLESLYETVLVDTPLAPYFKNCFDTAEELDDMNIEII
RNKLYKAYLEDFYNFVTEEIPEPAKECMQTLLGFEADRRSINIALNSLQSSDIDPDLKSD
LLPNIGKLYPLATFHLAQAQDFEGVRAALANVYEYRGFLETGNLEDHFYQLEMELCRDAF
TQQFAISTVWAWMKSKEQEVRNITWIAECIAQNQRERINNYISVY

Sequence of entity 8 (H, J, L), FASTA

>3J9V_8 V-type proton ATPase subunit G (chains H, J, L)
MSQKNGIATLLQAEKEAHEIVSKARKYRQDKLKQAKTDAAKEIDSYKIQKDKELKEFEQK
NAGGVGELEKKAEAGVQGELAEIKKIAEKKKDDVVKILIETVIKPSAEVHINAL

Sequence of entity 9 (G, I, K), FASTA

>3J9V_9 V-type proton ATPase subunit E (chains G, I, K)
MSSAITALTPNQVNDELNKMQAFIRKEAEEKAKEIQLKADQEYEIEKTNIVRNETNNIDG
NFKSKLKKAMLSQQITKSTIANKMRLKVLSAREQSLDGIFEETKEKLSGIANNRDEYKPI
LQSLIVEALLKLLEPKAIVKALERDVDLIESMKDDIMREYGEKAQRAPLEEIVISNDYLN
KDLVSGGVVVSNASDKIEINNTLEERLKLLSEEALPAIRLELYGPSKTRKFFD

Sequence of entity 10 (P), FASTA

>3J9V_10 V-type proton ATPase subunit H (chains P)
MGATKILMDSTHFNEIRSIIRSRSVAWDALARSEELSEIDASTAKALESILVKKNIGDGL
SSSNNAHSGFKVNGKTLIPLIHLLSTSDNEDCKKSVQNLIAELLSSDKYGDDTVKFFQED
PKQLEQLFDVSLKGDFQTVLISGFNVVSLLVQNGLHNVKLVEKLLKNNNLINILQNIEQM
DTCYVCIRLLQELAVIPEYRDVIWLHEKKFMPTLFKILQRATDSQLATRIVATNSNHLGI
QLQYHSLLLIWLLTFNPVFANELVQKYLSDFLDLLKLVKITIKEKVSRLCISIILQCCST
RVKQHKKVIKQLLLLGNALPTVQSLSERKYSDEELRQDISNLKEILENEYQELTSFDEYV
AELDSKLLCWSPPHVDNGFWSDNIDEFKKDNYKIFRQLIELLQAKVRNGDVNAKQEKIII
QVALNDITHVVELLPESIDVLDKTGGKADIMELLNHSDSRVKYEALKATQAIIGYTFK

Sequence of entity 11 (R, S, T, U, V, W, X, Y, Z, a), FASTA

>3J9V_11 V-type proton ATPase subunit c (chains R, S, T, U, V, W, X, Y, Z, a)
MTELCPVYAPFFGAIGCASAIIFTSLGAAYGTAKSGVGICATCVLRPDLLFKNIVPVIMA
GIIAIYGLVVSVLVCYSLGQKQALYTGFIQLGAGLSVGLSGLAAGFAIGIVGDAGVRGSS
QQPRLFVGMILILIFAEVLGLYGLIVALLLNSRATQDVVC

Primary citation

Electron cryomicroscopy observation of rotational states in a eukaryotic V-ATPase. Zhao, J., Benlekbir, S., Rubinstein, J.L. Nature (2015) 521:241-245. DOI 10.1038/nature14365 · PubMed

Other PDB entries of the same protein (UniProt P32563 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8EAS 2.6 Å, Yeast VO in complex with Vma12-22p
6M0R 2.7 Å, 2.7A Yeast Vo state3
7TAP 2.8 Å, Cryo-EM structure of archazolid A bound to yeast VO V-ATPase
6PE4 3.1 Å, Yeast Vo motor in complex with 1 VopQ molecule
8EAU 3.1 Å, Yeast VO in complex with Vma21p
6O7T 3.2 Å, Saccharomyces cerevisiae V-ATPase Vph1-VO
6PE5 3.2 Å, Yeast Vo motor in complex with 2 VopQ molecules
7TAO 3.2 Å, Cryo-EM structure of bafilomycin A1 bound to yeast VO V-ATPase
9E7L 3.33 Å, Yeast V-ATPase Vo proton channel bound to nanobody 2WVA7
9E76 3.4 Å, Yeast V-ATPase Vo proton channel bound to nanobody 1WVA25
6C6L 3.5 Å, Yeast Vacuolar ATPase Vo in lipid nanodisc
7TMR 3.5 Å, V-ATPase from Saccharomyces cerevisiae, State 1

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