9MOY: Reconstituted yeast V-ATPase

Reconstituted yeast V-ATPase bound to Rtc5p. Determined by electron microscopy at 3.6 Å resolution. Released 8 Apr 2026.

Method: Electron microscopy
Resolution: 3.6 Å
Organism: Saccharomyces cerevisiae
Chains: 32
Atoms: 68,913
Mol. weight: 1054.23 kDa
Ligands: ADP
Released: 8 Apr 2026

Explore 9MOY in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9MOY contains 441 α-helices and 298 β-strands across 32 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: 5 helices, 0 β-strands

Element	Residues	Length
α-helix	11-45	35
α-helix	49-52	4
α-helix	55-75	21
α-helix	84-118	35
α-helix	126-154	29

Chain A: 26 helices, 38 β-strands

Element	Residues	Length	Sheet
β-strand	25-31	7	1
β-strand	34-38	5	1
β-strand	44	1	2
β-strand	47-51	5	1
β-strand	56-64	9	1
β-strand	67-72	6	1
β-strand	80	1	3
β-strand	84-91	8	1
β-strand	93-96	4	4
β-strand	104-105	2	5
β-strand	111	1	5
α-helix	112-119	8
β-strand	123	1	6
β-strand	139-143	5	7
β-strand	151-153	3	8
β-strand	157-161	5	7
β-strand	170-173	4	7
β-strand	179-185	7	8
α-helix	186-187	2
β-strand	189-191	3	7
β-strand	198-202	5	8
β-strand	205-209	5	8
β-strand	213-216	4	4
α-helix	220-222	3
β-strand	225-226	2	5
β-strand	232	1	9
α-helix	238-243	6
β-strand	247	1	9
β-strand	251-255	5	5
α-helix	263-272	10
β-strand	277-282	6	5
β-strand	285	1	10
α-helix	287-296	10
α-helix	297-299	3
β-strand	301-302	2	11
β-strand	309-310	2	11
α-helix	311-314	4
β-strand	315-318	4	5
β-strand	321	1	10
α-helix	326-345	20
β-strand	349-355	7	5
α-helix	357-370	14
α-helix	373-375	3
α-helix	384-392	9
β-strand	396-399	4	5
α-helix	400	1
β-strand	407-416	10	5
α-helix	426-434	9
β-strand	437-438	2	5
β-strand	441	1	12
α-helix	443-446	4
β-strand	454	1	12
β-strand	460-461	2	5
α-helix	468-474	7
α-helix	478-502	25
α-helix	504-506	3
α-helix	509-521	13
α-helix	522-526	5
α-helix	540-562	23
α-helix	567-573	7
α-helix	575-583	9
α-helix	584-586	3
α-helix	589-591	3
α-helix	593-613	21

Chain b: 6 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	2	1	80
β-strand	5	1	80
α-helix	9-43	35
α-helix	50-53	4
α-helix	55-75	21
α-helix	84-119	36
α-helix	123-125	3
α-helix	126-156	31

Chain B: 25 helices, 33 β-strands

Element	Residues	Length	Sheet
α-helix	11-18	8
β-strand	26-28	3	1
β-strand	31-35	5	1
β-strand	38-41	4	1
β-strand	48	1	3
β-strand	52-56	5	1
β-strand	62-71	10	1
β-strand	74-79	6	1
β-strand	92-95	4	1
β-strand	101-104	4	23
α-helix	106-108	3
β-strand	111-114	4	24
β-strand	119	1	24
α-helix	124-126	3
β-strand	130-133	4	23
α-helix	138	1
β-strand	139	1	6
α-helix	140	1
α-helix	141-143	3
β-strand	144	1	25
β-strand	150-151	2	26
β-strand	152	1	27
α-helix	156-159	4
β-strand	164-165	2	26
β-strand	169	1	24
β-strand	172-174	3	28
α-helix	180-190	11
β-strand	192	1	27
β-strand	208-217	10	24
α-helix	219-230	12
α-helix	235-237	3
β-strand	238-244	7	24
α-helix	249-270	22
β-strand	273-278	6	24
α-helix	282-294	13
α-helix	297-298	2
β-strand	299	1	29
α-helix	301-303	3
β-strand	305	1	29
α-helix	308-316	9
β-strand	320-321	2	24
β-strand	322	1	25
β-strand	328-333	6	24
β-strand	334-336	3	28
α-helix	345-353	9
β-strand	356-360	5	28
α-helix	362-365	4
β-strand	373-380	8	28
α-helix	383-386	4
β-strand	388	1	30
β-strand	391	1	30
α-helix	396-420	25
α-helix	422-424	3
α-helix	427-438	12
α-helix	439-444	6
α-helix	454-465	12
α-helix	470-472	3
α-helix	478-484	7

Chain c: 5 helices, 0 β-strands

Element	Residues	Length
α-helix	10-43	34
α-helix	47-49	3
α-helix	55-75	21
α-helix	84-117	34
α-helix	126-154	29

Chain C: 27 helices, 37 β-strands

Element	Residues	Length	Sheet
β-strand	25-31	7	1
β-strand	34-38	5	1
β-strand	48-51	4	1
β-strand	56-64	9	1
β-strand	67-72	6	1
β-strand	80	1	13
β-strand	84-87	4	1
β-strand	93-96	4	14
β-strand	104-105	2	15
β-strand	111	1	15
α-helix	112-119	8
β-strand	123	1	16
β-strand	139-143	5	17
β-strand	151-153	3	18
β-strand	157-161	5	17
β-strand	170-173	4	17
α-helix	174-175	2
β-strand	179-185	7	18
α-helix	186-187	2
β-strand	189-191	3	17
β-strand	198-201	4	18
β-strand	206-209	4	18
β-strand	213-216	4	14
α-helix	220-222	3
β-strand	225-227	3	15
β-strand	232	1	19
α-helix	238	1
α-helix	239-243	5
β-strand	247	1	19
β-strand	251-255	5	15
α-helix	256-258	3
α-helix	262-271	10
β-strand	277-285	9	15
α-helix	287-294	8
α-helix	297-299	3
β-strand	301-302	2	20
β-strand	309-310	2	20
α-helix	311-314	4
β-strand	315-321	7	15
α-helix	326-345	20
β-strand	349-354	6	15
α-helix	357-371	15
β-strand	377	1	21
β-strand	380	1	21
α-helix	383-392	10
β-strand	396-399	4	15
α-helix	400	1
β-strand	407-416	10	15
α-helix	426-432	7
β-strand	437-438	2	15
β-strand	441	1	22
α-helix	443-447	5
β-strand	454	1	22
β-strand	460-461	2	15
α-helix	464-471	8
α-helix	478-502	25
α-helix	504-506	3
α-helix	509-524	16
α-helix	540-562	23
α-helix	567-573	7
α-helix	575-583	9
α-helix	584-586	3
α-helix	589-591	3
α-helix	593-614	22

Chain d: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	4-24	21
α-helix	30-33	4
α-helix	37-52	16
α-helix	53-55	3
β-strand	63-64	2	81
β-strand	67	1	82

Chain D: 23 helices, 31 β-strands

Element	Residues	Length	Sheet
α-helix	11-19	9
β-strand	26-28	3	1
β-strand	31-35	5	1
β-strand	38-41	4	1
β-strand	48	1	13
β-strand	52-56	5	1
β-strand	62-71	10	1
β-strand	74-79	6	1
β-strand	87	1	31
β-strand	92-95	4	1
β-strand	101-104	4	41
α-helix	106-108	3
β-strand	111-113	3	42
β-strand	119	1	42
β-strand	130-133	4	41
α-helix	138	1
β-strand	139	1	16
α-helix	140	1
α-helix	141-143	3
β-strand	144-145	2	43
β-strand	150-151	2	44
α-helix	156-158	3
β-strand	164-165	2	44
β-strand	169	1	42
β-strand	172-174	3	45
α-helix	180-190	11
β-strand	193	1	44
β-strand	208-217	10	42
α-helix	219-231	13
α-helix	234-237	4
β-strand	238-244	7	42
α-helix	249-269	21
β-strand	273-278	6	42
α-helix	281-294	14
β-strand	299	1	46
α-helix	301-303	3
β-strand	305	1	46
α-helix	308-316	9
β-strand	321-322	2	43
β-strand	325	1	43
β-strand	328-331	4	42
β-strand	334-336	3	45
α-helix	345-352	8
β-strand	356-360	5	45
α-helix	362-366	5
β-strand	373-380	8	45
α-helix	383-385	3
α-helix	396-420	25
α-helix	422-424	3
α-helix	427-438	12
α-helix	439-444	6
α-helix	454-465	12
α-helix	470-472	3
α-helix	478-484	7

24 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
H(+)-transporting two-sector ATPase	A, C, E	protein	617	Saccharomyces cerevisiae	B3LH69 (AlphaFold model)
V-type proton ATPase subunit E	G, I, K	protein	233	Saccharomyces cerevisiae	P22203 (AlphaFold model)
V-type proton ATPase subunit G	H, J, L	protein	114	Saccharomyces cerevisiae	P48836 (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
V-type proton ATPase subunit C	O	protein	392	Saccharomyces cerevisiae	P31412
Restriction of telomere capping protein 5	R	protein	567	Saccharomyces cerevisiae	Q12108
V-type proton ATPase subunit d	S	protein	345	Saccharomyces cerevisiae	P32366
V-type proton ATPase subunit c''	T	protein	213	Saccharomyces cerevisiae	P23968
V-type proton ATPase subunit c'	U	protein	164	Saccharomyces cerevisiae	P32842
V-type proton ATPase subunit c	V, W, X, Y, Z, a, b, c	protein	160	Saccharomyces cerevisiae	P25515
V-type proton ATPase subunit e	d	protein	73	Saccharomyces cerevisiae	Q3E7B6

5 more molecules are not listed.

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

>9MOY_1 H(+)-transporting two-sector ATPase (chains A, C, E)
MAGAIENARKEIKRISLEDHAESEYGAIYSVSGPVVIAENMIGCAMYELVKVGHDNLVGE
VIRIDGDKATIQVYEETAGLTVGDPVLRTGKPLSVELGPGLMETIYDGIQRPLKAIKEES
QSIYIPRGIDTPALDRTIKWQFTPGKFQVGDHISGGDIYGSVFENSLISSHKILLPPRSR
GTITWIAPAGEYTLDEKILEVEFDGKKSDFTLYHTWPVRVPRPVTEKLSADYPLLTGQRV
LDALFPCVQGGTTCIPGAFGCGKTVISQSLSKYSNSDAIIYVGCGERGNEMAEVLMEFPE
LYTEMSGTKEPIMKRTTLVANTSNMPVAAREASIYTGITLAEYFRDQGKNVSMIADSSSR
WAEALREISGRLGEMPADQGFPAYLGAKLASFYERAGKAVALGSPDRTGSVSIVAAVSPA
GGDFSDPVTTATLGITQVFWGLDKKLAQRKHFPSINTSVSYSKYTNVLNKFYDSNYPEFP
VLRDRMKEILSNAEELEQVVQLVGKSALSDSDKITLDVATLIKEDFLQQNGYSTYDAFCP
IWKTFDMMRAFISYHDEAQKAVANGANWSKLADSTGDVKHAVSSSKFFEPSRGEKEVHGE
FEKLLSTMQERFAESTD

Sequence of entity 2 (G, I, K), FASTA

>9MOY_2 V-type proton ATPase subunit E (chains G, I, K)
MSSAITALTPNQVNDELNKMQAFIRKEAEEKAKEIQLKADQEYEIEKTNIVRNETNNIDG
NFKSKLKKAMLSQQITKSTIANKMRLKVLSAREQSLDGIFEETKEKLSGIANNRDEYKPI
LQSLIVEALLKLLEPKAIVKALERDVDLIESMKDDIMREYGEKAQRAPLEEIVISNDYLN
KDLVSGGVVVSNASDKIEINNTLEERLKLLSEEALPAIRLELYGPSKTRKFFD

Sequence of entity 3 (H, J, L), FASTA

>9MOY_3 V-type proton ATPase subunit G (chains H, J, L)
MSQKNGIATLLQAEKEAHEIVSKARKYRQDKLKQAKTDAAKEIDSYKIQKDKELKEFEQK
NAGGVGELEKKAEAGVQGELAEIKKIAEKKKDDVVKILIETVIKPSAEVHINAL

Sequence of entity 4 (M), FASTA

>9MOY_4 V-type proton ATPase subunit D (chains M)
MSGNREQVFPTRMTLGLMKTKLKGANQGYSLLKRKSEALTKRFRDITKRIDDAKQKMGRV
MQTAAFSLAEVSYATGENIGYQVQESVSTARFKVRARQENVSGVYLSQFESYIDPEINDF
RLTGLGRGGQQVQRAKEIYSRAVETLVELASLQTAFIILDEVIKVTNRRVNAIEHVIIPR
TENTIAYINSELDELDREEFYRLKKVQEKKQNETAKLDAEMKLKRDRAEQDASEVAADEE
PQGETLVADQEDDVIF

Sequence of entity 5 (N), FASTA

>9MOY_5 V-type proton ATPase subunit F (chains N)
MAEKRTLIAVIADEDTTTGLLLAGIGQITPETQEKNFFVYQEGKTTKEEITDKFNHFTEE
RDDIAILLINQHIAENIRARVDSFTNAFPAILEIPSKDHPYDPEKDSVLKRVRKLFGE

Sequence of entity 6 (O), FASTA

>9MOY_6 V-type proton ATPase subunit C (chains O)
MATALYTANDFILISLPQNAQPVTAPGSKTDSWFNETLIGGRAFVSDFKIPEFKIGSLDT
LIVESEELSKVDNQIGASIGKIIEILQGLNETSTNAYRTLPINNMPVPEYLENFQWQTRK
FKLDKSIKDLITLISNESSQLDADVRATYANYNSAKTNLAAAERKKTGDLSVRSLHDIVK
PEDFVLNSEHLTTVLVAVPKSLKSDFEKSYETLSKNVVPASASVIAEDAEYVLFNVHLFK
KNVQEFTTAAREKKFIPREFNYSEELIDQLKKEHDSAASLEQSLRVQLVRLAKTAYVDVF
INWFHIKALRVYVESVLRYGLPPHFNIKIIAVPPKNLSKCKSELIDAFGFLGGNAFMKDK
KGKINKQDTSLHQYASLVDTEYEPFVMYIINL

Sequence of entity 7 (R), FASTA

>9MOY_7 Restriction of telomere capping protein 5 (chains R)
MGQSSSISSSNEEGSSHSKKFTNSKDILAYFNNKAQQQVTIPELVSFKGNLQIEDLNTPI
SHKALCNSLYFPQNHAMIVGIVTNMLRVLSNFPLMKSSYEPITGYGLLKCILLLNRARCA
KFLKTKSYDQLKLLFISLSLQKTDKEELSEESENDGNKELTIKQIITGFDDVDTEMLCIP
ADFMLQFLTWLLILTVDCPTTNSKLDNTETHDQWGNFKVSALNLLRTMNPDVVGDIESHS
ITFQQFSTAIRTVMPNLLKPLENLMEHFFYLQHDLVDHDTNLSSIQDSKVMTPALLAQLS
TGLPKELFIHKLQSLYIGRKSGFSMRSLQAKVFKWMAPSILVVSGMRITNSEEYAAEKNP
RYRHFLEEFPKLKESDQMMDASHLNKRKTTFAVYIDDPWKVTNKDYFGDLNTRIIEISPR
QDIYKVNQKGTIYFNTIGGGIGIGDKQPLIKPASKRYIPGNVSLTFDSTLEFAVFRNTGY
GGSLDPGLLSMERKEENSPYELHFLIQDVEVWGCGGEKELEEQIKQLEWEEAESKRRQQI
NLRSLGEDRALLEMAGLVGQHQGGGSM

Sequence of entity 8 (S), FASTA

>9MOY_8 V-type proton ATPase subunit d (chains S)
MEGVYFNIDNGFIEGVVRGYRNGLLSNNQYINLTQCDTLEDLKLQLSSTDYGNFLSSVSS
ESLTTSLIQEYASSKLYHEFNYIRDQSSGSTRKFMDYITYGYMIDNVALMITGTIHDRDK
GEILQRCHPLGWFDTLPTLSVATDLESLYETVLVDTPLAPYFKNCFDTAEELDDMNIEII
RNKLYKAYLEDFYNFVTEEIPEPAKECMQTLLGFEADRRSINIALNSLQSSDIDPDLKSD
LLPNIGKLYPLATFHLAQAQDFEGVRAALANVYEYRGFLETGNLEDHFYQLEMELCRDAF
TQQFAISTVWAWMKSKEQEVRNITWIAECIAQNQRERINNYISVY

Sequence of entity 9 (T), FASTA

>9MOY_9 V-type proton ATPase subunit c'' (chains T)
MNKESKDDDMSLGKFSFSHFLYYLVLIVVIVYGLYKLFTGHGSDINFGKFLLRTSPYMWA
NLGIALCVGLSVVGAAWGIFITGSSMIGAGVRAPRITTKNLISIIFCEVVAIYGLIIAIV
FSSKLTVATAENMYSKSNLYTGYSLFWAGITVGASNLICGIAVGITGATAAISDAADSAL
FVKILVIEIFGSILGLLGLIVGLLMAGKASEFQ

Sequence of entity 10 (U), FASTA

>9MOY_10 V-type proton ATPase subunit c' (chains U)
MSTQLASNIYAPLYAPFFGFAGCAAAMVLSCLGAAIGTAKSGIGIAGIGTFKPELIMKSL
IPVVMSGILAIYGLVVAVLIAGNLSPTEDYTLFNGFMHLSCGLCVGFACLSSGYAIGMVG
DVGVRKYMHQPRLFVGIVLILIFSEVLGLYGMIVALILNTRGSE

Sequence of entity 11 (V, W, X, Y, Z, a, b, c), FASTA

>9MOY_11 V-type proton ATPase subunit c (chains V, W, X, Y, Z, a, b, c)
MTELCPVYAPFFGAIGCASAIIFTSLGAAYGTAKSGVGICATCVLRPDLLFKNIVPVIMA
GIIAIYGLVVSVLVCYSLGQKQALYTGFIQLGAGLSVGLSGLAAGFAIGIVGDAGVRGSS
QQPRLFVGMILILIFAEVLGLYGLIVALLLNSRATQDVVC

Sequence of entity 12 (d), FASTA

>9MOY_12 V-type proton ATPase subunit e (chains d)
MSSFYTVVGVFIVVSAMSVLFWIMAPKNNQAVWRSTVILTLAMMFLMWAITFLCQLHPLV
APRRSDLRPEFAE

Ligands and cofactors

ID	Name	Formula	Copies
ADP	Adenosine-5'-diphosphate	C10 H15 N5 O10 P2	1

Primary citation

TLDc Protein Rtc5p Assembles Yeast V-ATPase. Wilkens, S., Khan, M.M. To be published.

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

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)
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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