5VOZ: Yeast V-ATPase

Yeast V-ATPase in complex with Legionella pneumophila effector SidK (rotational state 3). Determined by electron microscopy at 7.6 Å resolution. Released 28 Jun 2017.

Method: Electron microscopy
Resolution: 7.6 Å
Organisms: Saccharomyces cerevisiae (strain ATCC 204508 / S288c), Legionella pneumophila subsp. pneumophila ATCC 43290
Chains: 33
Atoms: 34,724
Mol. weight: 1151.45 kDa
Released: 28 Jun 2017

Explore 5VOZ in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5VOZ contains 391 α-helices and 218 β-strands across 33 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: 11 helices, 0 β-strands

Element	Residues	Length
α-helix	14-42	29
α-helix	47-49	3
α-helix	50-53	4
α-helix	55-60	6
α-helix	61-63	3
α-helix	64-76	13
α-helix	85-87	3
α-helix	89-121	33
α-helix	123-125	3
α-helix	126-134	9
α-helix	137-152	16

Chain A: 25 helices, 36 β-strands

Element	Residues	Length	Sheet
β-strand	26	1	1
β-strand	27-32	6	2
β-strand	35-39	5	2
β-strand	48-52	5	2
β-strand	57-65	9	2
β-strand	68-73	6	2
α-helix	80	1
β-strand	81	1	3
β-strand	86	1	1
β-strand	88-92	5	2
β-strand	94-97	4	4
β-strand	105-106	2	5
β-strand	112	1	5
α-helix	113-119	7
α-helix	125-126	2
β-strand	140-142	3	6
β-strand	143-144	2	7
β-strand	152-153	2	8
β-strand	158	1	9
β-strand	160-161	2	7
β-strand	162	1	10
β-strand	171	1	10
β-strand	174	1	9
α-helix	175-176	2
β-strand	181-186	6	8
β-strand	190-192	3	6
β-strand	199-202	4	8
β-strand	208-210	3	8
β-strand	214-217	4	4
α-helix	221-222	2
β-strand	227	1	11
β-strand	233	1	12
α-helix	239-244	6
β-strand	248	1	12
β-strand	252-256	5	5
α-helix	263-273	11
β-strand	278-283	6	5
α-helix	743-754	12
α-helix	765-768	4
β-strand	770-774	5	5
α-helix	781-801	21
β-strand	804-809	6	5
α-helix	812-826	15
α-helix	839-847	9
β-strand	853-854	2	11
α-helix	855	1
β-strand	862-863	2	11
β-strand	864-871	8	5
α-helix	881-889	9
β-strand	892-893	2	5
α-helix	898-900	3
α-helix	901-905	5
α-helix	919-928	10
α-helix	933-956	24
α-helix	959-961	3
α-helix	965-976	12
α-helix	977-981	5
α-helix	995-1017	23
α-helix	1022-1029	8
α-helix	1031-1037	7
α-helix	1053-1069	17

Chain b: 26 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	15-21	7	20
α-helix	26-34	9
β-strand	39-44	6	20
α-helix	57-79	23
α-helix	82-84	3
α-helix	94-99	6
α-helix	107-150	44
β-strand	185-191	7	21
α-helix	194-208	15
β-strand	215-218	4	21
β-strand	235-241	7	21
α-helix	246-255	10
β-strand	261	1	21
α-helix	273-322	50
α-helix	327-330	4
β-strand	335-341	7	20
α-helix	343-349	7
α-helix	410-419	10
α-helix	429-436	8
α-helix	438-441	4
α-helix	454-460	7
α-helix	462-478	17
α-helix	531-558	28
α-helix	578-593	16
α-helix	608-613	6
α-helix	632-656	25
α-helix	711-731	21
α-helix	732-734	3
α-helix	735-751	17
α-helix	755-760	6
α-helix	764-791	28
α-helix	794-806	13
α-helix	817-827	11

Chain B: 20 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	30-35	6	13
β-strand	38-42	5	13
β-strand	48	1	3
β-strand	51-56	6	13
β-strand	62-70	9	13
β-strand	75-79	5	13
β-strand	92-99	8	13
β-strand	101-104	4	14
β-strand	112-114	3	15
β-strand	130-133	4	14
β-strand	150	1	16
α-helix	156-162	7
β-strand	165	1	16
β-strand	169	1	15
α-helix	171	1
β-strand	172-174	3	17
α-helix	180-190	11
α-helix	194-201	8
β-strand	208-214	7	15
α-helix	219-232	14
β-strand	238-242	5	15
α-helix	249-270	22
β-strand	273-279	7	15
α-helix	281-290	10
β-strand	299	1	18
α-helix	301-303	3
β-strand	305	1	18
α-helix	308-315	8
α-helix	316-318	3
β-strand	320-321	2	15
α-helix	322	1
β-strand	328-331	4	15
β-strand	334-336	3	17
α-helix	345-353	9
β-strand	356-360	5	19
α-helix	361	1
α-helix	362-367	6
β-strand	373-380	8	19
α-helix	383-386	4
α-helix	396-419	24
α-helix	427-440	14
α-helix	454-464	11
α-helix	465-467	3
α-helix	478-483	6

Chain c: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	8-17	10
α-helix	30-45	16

Chain C: 25 helices, 32 β-strands

Element	Residues	Length	Sheet
β-strand	26-32	7	13
β-strand	35-39	5	13
β-strand	48-52	5	13
β-strand	57-65	9	13
β-strand	68-73	6	13
β-strand	85-92	8	13
β-strand	94-97	4	22
β-strand	105-106	2	23
β-strand	112	1	23
α-helix	114-115	2
α-helix	116-120	5
β-strand	140-142	3	24
β-strand	143-144	2	25
β-strand	152-154	3	26
β-strand	158	1	27
β-strand	160-161	2	25
β-strand	174	1	27
α-helix	175-176	2
β-strand	180-186	7	26
β-strand	190-192	3	24
β-strand	199-202	4	26
β-strand	206-210	5	26
β-strand	214-217	4	22
α-helix	221-223	3
β-strand	226-227	2	28
β-strand	233	1	29
α-helix	239-244	6
β-strand	248	1	29
β-strand	252-255	4	23
α-helix	263-272	10
β-strand	278-282	5	23
α-helix	743-754	12
α-helix	756-757	2
α-helix	765-768	4
β-strand	770-773	4	23
α-helix	781-785	5
α-helix	787-800	14
β-strand	804-809	6	23
α-helix	812-826	15
α-helix	832-834	3
α-helix	838-848	11
β-strand	853-854	2	28
α-helix	855	1
β-strand	862-863	2	28
β-strand	864-870	7	23
α-helix	881-889	9
β-strand	892-894	3	23
α-helix	898-902	5
β-strand	914-915	2	23
α-helix	919-929	11
α-helix	933-956	24
α-helix	964-981	18
α-helix	988-990	3
α-helix	995-1017	23
α-helix	1022-1029	8
α-helix	1031-1037	7
α-helix	1053-1069	17

Chain d: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	2-25	24
α-helix	79-98	20

Chain D: 17 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	31-35	5	2
β-strand	38-41	4	2
α-helix	48	1
β-strand	51-56	6	2
β-strand	62-71	10	2
β-strand	74-79	6	2
β-strand	92-99	8	2
β-strand	101-104	4	30
β-strand	112-114	3	31
β-strand	119	1	31
β-strand	130-133	4	30
α-helix	150-152	3
α-helix	156-161	6
β-strand	172-174	3	32
α-helix	180-190	11
α-helix	194-200	7
β-strand	208-215	8	31
α-helix	219-232	14
β-strand	239-243	5	31
α-helix	249-270	22
β-strand	273-279	7	31
α-helix	281-290	10
α-helix	297-298	2
β-strand	299	1	33
α-helix	301-303	3
β-strand	305	1	33
α-helix	308-317	10
β-strand	320-321	2	31
β-strand	328-331	4	31
β-strand	334-336	3	32
α-helix	345-353	9
β-strand	356-360	5	32
α-helix	362-367	6
β-strand	373-380	8	32
α-helix	396-419	24
α-helix	428-442	15
α-helix	454-464	11
α-helix	478-483	6

25 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 catalytic subunit A,V-type proton ATPase catalytic subunit A	A, C, E	protein	617	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	B3LH69 (AlphaFold model)
V-type proton ATPase subunit B	B, D, F	protein	517	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P16140 (AlphaFold model)
V-type proton ATPase subunit E	G, I, K	protein	233	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P22203 (AlphaFold model)
V-type proton ATPase subunit G	H, J, L	protein	114	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P48836 (AlphaFold model)
V-type proton ATPase subunit D	M	protein	256	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P32610
V-type proton ATPase subunit F	N	protein	118	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P39111
V-type proton ATPase subunit C	O	protein	392	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P31412
V-type proton ATPase subunit H	P	protein	478	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P41807
V-type proton ATPase subunit d	Q	protein	345	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P32366
V-type proton ATPase subunit c''	R	protein	213	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P23968
V-type proton ATPase subunit c'	S	protein	164	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P32842
V-type proton ATPase subunit c	T, U, V, W, X, Y, Z, a	protein	160	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P25515

4 more molecules are not listed.

Sequence of entity 1 (A, C, E), FASTA

>5VOZ_1 V-type proton ATPase catalytic subunit A,V-type proton ATPase catalytic subunit A (chains A, C, E)
MAGAIENARKEIKRISLEDHAESEYGAIYSVSGPVVIAENMIGCAMYELVKVGHDNLVGE
VIRIDGDKATIQVYEETAGLTVGDPVLRTGKPLSVELGPGLMETIYDGIQRPLKAIKEES
QSIYIPRGIDTPALDRTIKWQFTPGKFQVGDHISGGDIYGSVFENSLISSHKILLPPRSR
GTITWIAPAGEYTLDEKILEVEFDGKKSDFTLYHTWPVRVPRPVTEKLSADYPLLTGQRV
LDALFPCVQGGTTCIPGAFGCGKTVISQSLSKYSNSDAIIYVGCGERGNEMAEVLMEFPE
LYTEMSGTKEPIMKRTTLVANTSNMPVAAREASIYTGITLAEYFRDQGKNVSMIADSSSR
WAEALREISGRLGEMPADQGFPAYLGAKLASFYERAGKAVALGSPDRTGSVSIVAAVSPA
GGDFSDPVTTATLGITQVFWGLDKKLAQRKHFPSINTSVSYSKYTNVLNKFYDSNYPEFP
VLRDRMKEILSNAEELEQVVQLVGKSALSDSDKITLDVATLIKEDFLQQNGYSTYDAFCP
IWKTFDMMRAFISYHDEAQKAVANGANWSKLADSTGDVKHAVSSSKFFEPSRGEKEVHGE
FEKLLSTMQERFAESTD

Sequence of entity 2 (B, D, F), FASTA

>5VOZ_2 V-type proton ATPase subunit B (chains B, D, F)
MVLSDKELFAINKKAVEQGFNVKPRLNYNTVSGVNGPLVILEKVKFPRYNEIVNLTLPDG
TVRQGQVLEIRGDRAIVQVFEGTSGIDVKKTTVEFTGESLRIPVSEDMLGRIFDGSGRPI
DNGPKVFAEDYLDINGSPINPYARIYPEEMISTGVSAIDTMNSIARGQKIPIFSASGLPH
NEIAAQICRQAGLVRPTKDVHDGHEENFSIVFAAMGVNLETARFFKQDFEENGSLERTSL
FLNLANDPTIERIITPRLALTTAEYLAYQTERHVLTILTDMSSYADALREVSAAREEVPG
RRGYPGYMYTDLSTIYERAGRVEGRNGSITQIPILTMPNDDITHPIPDLTGYITEGQIFV
DRQLHNKGIYPPINVLPSLSRLMKSAIGEGMTRKDHGDVSNQLYAKYAIGKDAAAMKAVV
GEEALSIEDKLSLEFLEKFEKTFITQGAYEDRTVFESLDQAWSLLRIYPKEMLNRISPKI
LDEFYDRARDDADEDEEDPDTRSSGKKKDASQEESLI

Sequence of entity 3 (G, I, K), FASTA

>5VOZ_3 V-type proton ATPase subunit E (chains G, I, K)
MSSAITALTPNQVNDELNKMQAFIRKEAEEKAKEIQLKADQEYEIEKTNIVRNETNNIDG
NFKSKLKKAMLSQQITKSTIANKMRLKVLSAREQSLDGIFEETKEKLSGIANNRDEYKPI
LQSLIVEALLKLLEPKAIVKALERDVDLIESMKDDIMREYGEKAQRAPLEEIVISNDYLN
KDLVSGGVVVSNASDKIEINNTLEERLKLLSEEALPAIRLELYGPSKTRKFFD

Sequence of entity 4 (H, J, L), FASTA

>5VOZ_4 V-type proton ATPase subunit G (chains H, J, L)
MSQKNGIATLLQAEKEAHEIVSKARKYRQDKLKQAKTDAAKEIDSYKIQKDKELKEFEQK
NAGGVGELEKKAEAGVQGELAEIKKIAEKKKDDVVKILIETVIKPSAEVHINAL

Sequence of entity 5 (M), FASTA

>5VOZ_5 V-type proton ATPase subunit D (chains M)
MSGNREQVFPTRMTLGLMKTKLKGANQGYSLLKRKSEALTKRFRDITKRIDDAKQKMGRV
MQTAAFSLAEVSYATGENIGYQVQESVSTARFKVRARQENVSGVYLSQFESYIDPEINDF
RLTGLGRGGQQVQRAKEIYSRAVETLVELASLQTAFIILDEVIKVTNRRVNAIEHVIIPR
TENTIAYINSELDELDREEFYRLKKVQEKKQNETAKLDAEMKLKRDRAEQDASEVAADEE
PQGETLVADQEDDVIF

Sequence of entity 6 (N), FASTA

>5VOZ_6 V-type proton ATPase subunit F (chains N)
MAEKRTLIAVIADEDTTTGLLLAGIGQITPETQEKNFFVYQEGKTTKEEITDKFNHFTEE
RDDIAILLINQHIAENIRARVDSFTNAFPAILEIPSKDHPYDPEKDSVLKRVRKLFGE

Sequence of entity 7 (O), FASTA

>5VOZ_7 V-type proton ATPase subunit C (chains O)
MATALYTANDFILISLPQNAQPVTAPGSKTDSWFNETLIGGRAFVSDFKIPEFKIGSLDT
LIVESEELSKVDNQIGASIGKIIEILQGLNETSTNAYRTLPINNMPVPEYLENFQWQTRK
FKLDKSIKDLITLISNESSQLDADVRATYANYNSAKTNLAAAERKKTGDLSVRSLHDIVK
PEDFVLNSEHLTTVLVAVPKSLKSDFEKSYETLSKNVVPASASVIAEDAEYVLFNVHLFK
KNVQEFTTAAREKKFIPREFNYSEELIDQLKKEHDSAASLEQSLRVQLVRLAKTAYVDVF
INWFHIKALRVYVESVLRYGLPPHFNIKIIAVPPKNLSKCKSELIDAFGFLGGNAFMKDK
KGKINKQDTSLHQYASLVDTEYEPFVMYIINL

Sequence of entity 8 (P), FASTA

>5VOZ_8 V-type proton ATPase subunit H (chains P)
MGATKILMDSTHFNEIRSIIRSRSVAWDALARSEELSEIDASTAKALESILVKKNIGDGL
SSSNNAHSGFKVNGKTLIPLIHLLSTSDNEDCKKSVQNLIAELLSSDKYGDDTVKFFQED
PKQLEQLFDVSLKGDFQTVLISGFNVVSLLVQNGLHNVKLVEKLLKNNNLINILQNIEQM
DTCYVCIRLLQELAVIPEYRDVIWLHEKKFMPTLFKILQRATDSQLATRIVATNSNHLGI
QLQYHSLLLIWLLTFNPVFANELVQKYLSDFLDLLKLVKITIKEKVSRLCISIILQCCST
RVKQHKKVIKQLLLLGNALPTVQSLSERKYSDEELRQDISNLKEILENEYQELTSFDEYV
AELDSKLLCWSPPHVDNGFWSDNIDEFKKDNYKIFRQLIELLQAKVRNGDVNAKQEKIII
QVALNDITHVVELLPESIDVLDKTGGKADIMELLNHSDSRVKYEALKATQAIIGYTFK

Sequence of entity 9 (Q), FASTA

>5VOZ_9 V-type proton ATPase subunit d (chains Q)
MEGVYFNIDNGFIEGVVRGYRNGLLSNNQYINLTQCDTLEDLKLQLSSTDYGNFLSSVSS
ESLTTSLIQEYASSKLYHEFNYIRDQSSGSTRKFMDYITYGYMIDNVALMITGTIHDRDK
GEILQRCHPLGWFDTLPTLSVATDLESLYETVLVDTPLAPYFKNCFDTAEELDDMNIEII
RNKLYKAYLEDFYNFVTEEIPEPAKECMQTLLGFEADRRSINIALNSLQSSDIDPDLKSD
LLPNIGKLYPLATFHLAQAQDFEGVRAALANVYEYRGFLETGNLEDHFYQLEMELCRDAF
TQQFAISTVWAWMKSKEQEVRNITWIAECIAQNQRERINNYISVY

Sequence of entity 10 (R), FASTA

>5VOZ_10 V-type proton ATPase subunit c'' (chains R)
MNKESKDDDMSLGKFSFSHFLYYLVLIVVIVYGLYKLFTGHGSDINFGKFLLRTSPYMWA
NLGIALCVGLSVVGAAWGIFITGSSMIGAGVRAPRITTKNLISIIFCEVVAIYGLIIAIV
FSSKLTVATAENMYSKSNLYTGYSLFWAGITVGASNLICGIAVGITGATAAISDAADSAL
FVKILVIEIFGSILGLLGLIVGLLMAGKASEFQ

Sequence of entity 11 (S), FASTA

>5VOZ_11 V-type proton ATPase subunit c' (chains S)
MSTQLASNIYAPLYAPFFGFAGCAAAMVLSCLGAAIGTAKSGIGIAGIGTFKPELIMKSL
IPVVMSGILAIYGLVVAVLIAGNLSPTEDYTLFNGFMHLSCGLCVGFACLSSGYAIGMVG
DVGVRKYMHQPRLFVGIVLILIFSEVLGLYGMIVALILNTRGSE

Sequence of entity 12 (T, U, V, W, X, Y, Z, a), FASTA

>5VOZ_12 V-type proton ATPase subunit c (chains T, U, V, W, X, Y, Z, a)
MTELCPVYAPFFGAIGCASAIIFTSLGAAYGTAKSGVGICATCVLRPDLLFKNIVPVIMA
GIIAIYGLVVSVLVCYSLGQKQALYTGFIQLGAGLSVGLSGLAAGFAIGIVGDAGVRGSS
QQPRLFVGMILILIFAEVLGLYGLIVALLLNSRATQDVVC

Primary citation

Molecular basis for the binding and modulation of V-ATPase by a bacterial effector protein. Zhao, J., Beyrakhova, K., Liu, Y. et al. PLoS Pathog (2017) 13:e1006394-e1006394. DOI 10.1371/journal.ppat.1006394 · PubMed

Other PDB entries of the same protein (UniProt B3LH69 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9MOY 3.6 Å, Reconstituted yeast V-ATPase bound to Rtc5p
7TMS 3.8 Å, V-ATPase from Saccharomyces cerevisiae, State 2
7TMT 3.8 Å, V-ATPase from Saccharomyces cerevisiae, State 3
6O7V 6.6 Å, Saccharomyces cerevisiae V-ATPase Stv1-V1VO State 1
5VOX 6.8 Å, Yeast V-ATPase in complex with Legionella pneumophila effector SidK (rotational state 1)
6O7W 7.0 Å, Saccharomyces cerevisiae V-ATPase Stv1-V1VO State 2
5VOY 7.9 Å, Yeast V-ATPase in complex with Legionella pneumophila effector SidK (rotational state 2)
6O7X 8.7 Å, Saccharomyces cerevisiae V-ATPase Stv1-V1VO State 3

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