5VOY: Yeast V-ATPase

Yeast V-ATPase in complex with Legionella pneumophila effector SidK (rotational state 2). Determined by electron microscopy at 7.9 Å resolution. Released 21 Jun 2017.

Method: Electron microscopy
Resolution: 7.9 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: 21 Jun 2017

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

Secondary structure: helices and β-sheets

5VOY contains 389 α-helices and 210 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: 7 helices, 0 β-strands

Element	Residues	Length
α-helix	14-42	29
α-helix	55-60	6
α-helix	61-63	3
α-helix	64-76	13
α-helix	89-121	33
α-helix	125-135	11
α-helix	137-152	16

Chain A: 21 helices, 34 β-strands

Element	Residues	Length	Sheet
β-strand	26-32	7	1
β-strand	35-39	5	1
β-strand	48-52	5	1
β-strand	57-65	9	1
β-strand	68-73	6	1
β-strand	85-92	8	1
β-strand	94-97	4	2
β-strand	105-106	2	3
β-strand	112	1	3
α-helix	113-119	7
β-strand	140-144	5	4
β-strand	152-154	3	5
β-strand	158-162	5	4
β-strand	171-174	4	4
α-helix	175-176	2
β-strand	180-186	7	5
β-strand	190-192	3	4
β-strand	197-202	6	5
β-strand	206-211	6	5
β-strand	214-217	4	2
α-helix	221-223	3
β-strand	226-227	2	6
β-strand	233	1	7
α-helix	239-244	6
β-strand	248	1	7
β-strand	252-255	4	3
α-helix	263-272	10
β-strand	278-283	6	3
β-strand	740	1	8
α-helix	743-754	12
α-helix	765-768	4
β-strand	770-773	4	3
β-strand	776	1	8
α-helix	781-785	5
α-helix	787-801	15
β-strand	805-810	6	3
α-helix	812-826	15
β-strand	832	1	9
β-strand	835	1	9
α-helix	839-849	11
β-strand	853-854	2	6
α-helix	855	1
β-strand	862-863	2	6
β-strand	865-870	6	3
α-helix	881-889	9
β-strand	892-893	2	3
α-helix	898-901	4
β-strand	915-916	2	3
α-helix	919-926	8
α-helix	933-956	24
α-helix	964-980	17
α-helix	995-1015	21
α-helix	1022-1029	8
α-helix	1031-1037	7
α-helix	1056-1069	14

Chain b: 25 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	15-21	7	14
α-helix	26-36	11
β-strand	39-44	6	14
α-helix	57-78	22
α-helix	82-84	3
α-helix	94-99	6
α-helix	107-150	44
β-strand	185-191	7	15
α-helix	194-207	14
β-strand	216-218	3	15
β-strand	235-241	7	15
α-helix	246-254	9
β-strand	261	1	15
α-helix	274-323	50
α-helix	327-330	4
β-strand	335-341	7	14
α-helix	345-351	7
α-helix	411-419	9
α-helix	429-438	10
α-helix	443-447	5
α-helix	454-460	7
α-helix	462-478	17
α-helix	533-557	25
α-helix	578-593	16
α-helix	608-613	6
α-helix	632-642	11
α-helix	644-656	13
α-helix	711-731	21
α-helix	734-758	25
α-helix	764-790	27
α-helix	794-806	13
α-helix	818-827	10

Chain B: 17 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	30-35	6	1
β-strand	38-42	5	1
α-helix	48	1
β-strand	51-56	6	1
β-strand	62-71	10	1
β-strand	74-79	6	1
β-strand	92-99	8	1
β-strand	101-104	4	10
β-strand	114	1	11
β-strand	130-133	4	10
α-helix	156-160	5
β-strand	169	1	12
α-helix	171	1
β-strand	172-174	3	12
α-helix	180-200	21
β-strand	208-214	7	12
α-helix	219-232	14
β-strand	242	1	11
α-helix	249-253	5
α-helix	255-270	16
β-strand	273-279	7	12
α-helix	281-288	8
β-strand	299	1	13
α-helix	301-303	3
β-strand	305	1	13
α-helix	308-316	9
β-strand	320-321	2	12
β-strand	328-336	9	12
α-helix	345-353	9
β-strand	358-360	3	12
α-helix	362-367	6
β-strand	373-374	2	12
α-helix	383-386	4
α-helix	396-419	24
α-helix	427-442	16
α-helix	454-465	12
α-helix	478-483	6

Chain c: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	8-16	9
α-helix	30-46	17

Chain C: 24 helices, 30 β-strands

Element	Residues	Length	Sheet
β-strand	26-32	7	1
β-strand	35-39	5	1
β-strand	48-52	5	1
β-strand	57-65	9	1
β-strand	68-73	6	1
β-strand	85-92	8	1
β-strand	94-97	4	16
β-strand	105-106	2	17
β-strand	112	1	17
α-helix	113-119	7
α-helix	125-126	2
β-strand	139-142	4	18
β-strand	143-144	2	19
β-strand	152-153	2	20
β-strand	158	1	21
β-strand	160-161	2	19
β-strand	174	1	21
α-helix	175-176	2
β-strand	181-185	5	20
β-strand	190-193	4	18
β-strand	199-202	4	20
β-strand	206-210	5	20
β-strand	214-217	4	16
α-helix	221-223	3
β-strand	226-227	2	22
α-helix	239-244	6
β-strand	252-256	5	17
α-helix	263-273	11
β-strand	278-740	9	17
α-helix	743-754	12
α-helix	756-757	2
β-strand	770-776	7	17
α-helix	781-801	21
β-strand	804-810	7	17
α-helix	812-826	15
α-helix	832-834	3
α-helix	838-849	12
β-strand	853-854	2	22
α-helix	855-856	2
β-strand	862-863	2	22
β-strand	864-871	8	17
α-helix	881-889	9
β-strand	892-896	5	17
α-helix	898-902	5
β-strand	909-916	8	17
α-helix	919-929	11
α-helix	933-956	24
α-helix	964-976	13
α-helix	977-981	5
α-helix	995-1017	23
α-helix	1022-1029	8
α-helix	1031-1037	7
α-helix	1038-1040	3
α-helix	1053-1069	17

Chain d: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	2-26	25
α-helix	79-98	20

Chain D: 20 helices, 27 β-strands

Element	Residues	Length	Sheet
β-strand	31-35	5	1
β-strand	38-41	4	1
β-strand	51-56	6	1
β-strand	63-71	9	1
β-strand	74-79	6	1
β-strand	92-99	8	1
β-strand	101-104	4	23
β-strand	112-114	3	24
β-strand	119	1	24
β-strand	130-133	4	23
β-strand	150	1	25
α-helix	156-160	5
β-strand	165	1	25
β-strand	169	1	24
β-strand	172-174	3	26
α-helix	180-190	11
α-helix	194-200	7
β-strand	208-214	7	24
β-strand	217	1	27
α-helix	219-232	14
β-strand	238-242	5	24
β-strand	244	1	27
α-helix	249-253	5
α-helix	255-270	16
β-strand	273-279	7	24
α-helix	281-290	10
α-helix	298-299	2
α-helix	301-303	3
α-helix	308-315	8
β-strand	320-321	2	24
α-helix	322	1
β-strand	328-333	6	24
β-strand	334-336	3	26
α-helix	345-353	9
β-strand	356-357	2	28
β-strand	358-359	2	26
β-strand	360	1	29
α-helix	361	1
α-helix	362-367	6
β-strand	373	1	29
β-strand	379-380	2	28
α-helix	396-420	25
α-helix	427-439	13
α-helix	440-444	5
α-helix	454-464	11
α-helix	470-472	3
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

>5VOY_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

>5VOY_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

>5VOY_3 V-type proton ATPase subunit E (chains G, I, K)
MSSAITALTPNQVNDELNKMQAFIRKEAEEKAKEIQLKADQEYEIEKTNIVRNETNNIDG
NFKSKLKKAMLSQQITKSTIANKMRLKVLSAREQSLDGIFEETKEKLSGIANNRDEYKPI
LQSLIVEALLKLLEPKAIVKALERDVDLIESMKDDIMREYGEKAQRAPLEEIVISNDYLN
KDLVSGGVVVSNASDKIEINNTLEERLKLLSEEALPAIRLELYGPSKTRKFFD

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

>5VOY_4 V-type proton ATPase subunit G (chains H, J, L)
MSQKNGIATLLQAEKEAHEIVSKARKYRQDKLKQAKTDAAKEIDSYKIQKDKELKEFEQK
NAGGVGELEKKAEAGVQGELAEIKKIAEKKKDDVVKILIETVIKPSAEVHINAL

Sequence of entity 5 (M), FASTA

>5VOY_5 V-type proton ATPase subunit D (chains M)
MSGNREQVFPTRMTLGLMKTKLKGANQGYSLLKRKSEALTKRFRDITKRIDDAKQKMGRV
MQTAAFSLAEVSYATGENIGYQVQESVSTARFKVRARQENVSGVYLSQFESYIDPEINDF
RLTGLGRGGQQVQRAKEIYSRAVETLVELASLQTAFIILDEVIKVTNRRVNAIEHVIIPR
TENTIAYINSELDELDREEFYRLKKVQEKKQNETAKLDAEMKLKRDRAEQDASEVAADEE
PQGETLVADQEDDVIF

Sequence of entity 6 (N), FASTA

>5VOY_6 V-type proton ATPase subunit F (chains N)
MAEKRTLIAVIADEDTTTGLLLAGIGQITPETQEKNFFVYQEGKTTKEEITDKFNHFTEE
RDDIAILLINQHIAENIRARVDSFTNAFPAILEIPSKDHPYDPEKDSVLKRVRKLFGE

Sequence of entity 7 (O), FASTA

>5VOY_7 V-type proton ATPase subunit C (chains O)
MATALYTANDFILISLPQNAQPVTAPGSKTDSWFNETLIGGRAFVSDFKIPEFKIGSLDT
LIVESEELSKVDNQIGASIGKIIEILQGLNETSTNAYRTLPINNMPVPEYLENFQWQTRK
FKLDKSIKDLITLISNESSQLDADVRATYANYNSAKTNLAAAERKKTGDLSVRSLHDIVK
PEDFVLNSEHLTTVLVAVPKSLKSDFEKSYETLSKNVVPASASVIAEDAEYVLFNVHLFK
KNVQEFTTAAREKKFIPREFNYSEELIDQLKKEHDSAASLEQSLRVQLVRLAKTAYVDVF
INWFHIKALRVYVESVLRYGLPPHFNIKIIAVPPKNLSKCKSELIDAFGFLGGNAFMKDK
KGKINKQDTSLHQYASLVDTEYEPFVMYIINL

Sequence of entity 8 (P), FASTA

>5VOY_8 V-type proton ATPase subunit H (chains P)
MGATKILMDSTHFNEIRSIIRSRSVAWDALARSEELSEIDASTAKALESILVKKNIGDGL
SSSNNAHSGFKVNGKTLIPLIHLLSTSDNEDCKKSVQNLIAELLSSDKYGDDTVKFFQED
PKQLEQLFDVSLKGDFQTVLISGFNVVSLLVQNGLHNVKLVEKLLKNNNLINILQNIEQM
DTCYVCIRLLQELAVIPEYRDVIWLHEKKFMPTLFKILQRATDSQLATRIVATNSNHLGI
QLQYHSLLLIWLLTFNPVFANELVQKYLSDFLDLLKLVKITIKEKVSRLCISIILQCCST
RVKQHKKVIKQLLLLGNALPTVQSLSERKYSDEELRQDISNLKEILENEYQELTSFDEYV
AELDSKLLCWSPPHVDNGFWSDNIDEFKKDNYKIFRQLIELLQAKVRNGDVNAKQEKIII
QVALNDITHVVELLPESIDVLDKTGGKADIMELLNHSDSRVKYEALKATQAIIGYTFK

Sequence of entity 9 (Q), FASTA

>5VOY_9 V-type proton ATPase subunit d (chains Q)
MEGVYFNIDNGFIEGVVRGYRNGLLSNNQYINLTQCDTLEDLKLQLSSTDYGNFLSSVSS
ESLTTSLIQEYASSKLYHEFNYIRDQSSGSTRKFMDYITYGYMIDNVALMITGTIHDRDK
GEILQRCHPLGWFDTLPTLSVATDLESLYETVLVDTPLAPYFKNCFDTAEELDDMNIEII
RNKLYKAYLEDFYNFVTEEIPEPAKECMQTLLGFEADRRSINIALNSLQSSDIDPDLKSD
LLPNIGKLYPLATFHLAQAQDFEGVRAALANVYEYRGFLETGNLEDHFYQLEMELCRDAF
TQQFAISTVWAWMKSKEQEVRNITWIAECIAQNQRERINNYISVY

Sequence of entity 10 (R), FASTA

>5VOY_10 V-type proton ATPase subunit c'' (chains R)
MNKESKDDDMSLGKFSFSHFLYYLVLIVVIVYGLYKLFTGHGSDINFGKFLLRTSPYMWA
NLGIALCVGLSVVGAAWGIFITGSSMIGAGVRAPRITTKNLISIIFCEVVAIYGLIIAIV
FSSKLTVATAENMYSKSNLYTGYSLFWAGITVGASNLICGIAVGITGATAAISDAADSAL
FVKILVIEIFGSILGLLGLIVGLLMAGKASEFQ

Sequence of entity 11 (S), FASTA

>5VOY_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

>5VOY_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
5VOZ 7.6 Å, Yeast V-ATPase in complex with Legionella pneumophila effector SidK (rotational state 3)
6O7X 8.7 Å, Saccharomyces cerevisiae V-ATPase Stv1-V1VO State 3

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