9ODU: Yeast V-ATPase

Yeast V-ATPase bound to Rtc5p, rotary state 2. Determined by electron microscopy at 3.9 Å resolution. Released 29 Apr 2026.

Method: Electron microscopy
Resolution: 3.9 Å
Organism: Saccharomyces cerevisiae
Chains: 32
Atoms: 69,067
Mol. weight: 1054.23 kDa
Ligands: ADP
Released: 29 Apr 2026

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

Secondary structure: helices and β-sheets

9ODU contains 450 α-helices and 283 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: 6 helices, 0 β-strands

Element	Residues	Length
α-helix	10-45	36
α-helix	52-54	3
α-helix	55-75	21
α-helix	84-116	33
α-helix	117-120	4
α-helix	125-154	30

Chain A: 27 helices, 41 β-strands

Element	Residues	Length	Sheet
β-strand	25-31	7	1
β-strand	34-38	5	1
β-strand	47-51	5	1
β-strand	56-60	5	1
β-strand	62	1	1
β-strand	64	1	2
β-strand	67	1	2
β-strand	68-72	5	1
β-strand	80	1	3
β-strand	84-91	8	1
β-strand	93	1	4
β-strand	96	1	5
β-strand	104-105	2	6
β-strand	111	1	6
α-helix	112-119	8
β-strand	123	1	7
β-strand	139-143	5	8
β-strand	151-153	3	9
β-strand	159-161	3	8
β-strand	170-171	2	8
α-helix	172	1
β-strand	179-185	7	9
β-strand	189-191	3	8
β-strand	196-202	7	9
β-strand	205-210	6	9
β-strand	213	1	5
β-strand	216	1	4
α-helix	220-222	3
β-strand	225-226	2	10
α-helix	227-229	3
β-strand	232-233	2	11
α-helix	238-243	6
β-strand	246-247	2	11
β-strand	251-255	5	6
α-helix	262-272	11
β-strand	277-285	9	6
α-helix	287-299	13
β-strand	301-302	2	12
β-strand	309-310	2	12
α-helix	311-314	4
β-strand	315-321	7	6
α-helix	326-330	5
α-helix	332-344	13
β-strand	349-355	7	6
α-helix	357-371	15
α-helix	373-375	3
α-helix	383-393	11
β-strand	398-399	2	10
α-helix	400	1
β-strand	407-408	2	10
β-strand	409-416	8	6
α-helix	419-421	3
α-helix	426-434	9
β-strand	437-438	2	6
β-strand	441	1	13
α-helix	443-446	4
β-strand	454	1	13
β-strand	460	1	6
α-helix	464-474	11
α-helix	478-502	25
α-helix	504-506	3
α-helix	509-524	16
α-helix	533-536	4
α-helix	540-562	23
α-helix	567-573	7
α-helix	575-584	10
α-helix	589-591	3
α-helix	593-613	21

Chain b: 5 helices, 0 β-strands

Element	Residues	Length
α-helix	11-36	26
α-helix	39-45	7
α-helix	55-77	23
α-helix	84-121	38
α-helix	125-156	32

Chain B: 24 helices, 31 β-strands

Element	Residues	Length	Sheet
α-helix	10-13	4
α-helix	14-17	4
α-helix	24-25	2
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	101-102	2	43
α-helix	106-108	3
β-strand	112-113	2	44
β-strand	119	1	44
α-helix	124-126	3
β-strand	132-133	2	43
α-helix	138	1
β-strand	139	1	7
α-helix	140	1
β-strand	144-145	2	45
β-strand	150	1	46
β-strand	152	1	47
α-helix	156-160	5
β-strand	165	1	46
β-strand	169	1	44
β-strand	172-174	3	48
α-helix	180-188	9
β-strand	192	1	47
β-strand	208-217	10	44
α-helix	219-231	13
α-helix	234-236	3
β-strand	238-244	7	44
α-helix	249-270	22
β-strand	273-278	6	44
α-helix	282-295	14
β-strand	299	1	49
α-helix	301-303	3
β-strand	305	1	49
α-helix	308-317	10
β-strand	320	1	44
β-strand	321-322	2	45
β-strand	328-331	4	44
β-strand	334-336	3	48
α-helix	345-353	9
β-strand	356-360	5	48
α-helix	362-366	5
β-strand	373-380	8	48
α-helix	383-386	4
α-helix	396-420	25
α-helix	427-438	12
α-helix	439-444	6
α-helix	454-465	12
α-helix	470-472	3
α-helix	478-485	8

Chain c: 8 helices, 0 β-strands

Element	Residues	Length
α-helix	8-43	36
α-helix	49-52	4
α-helix	55-62	8
α-helix	65-75	11
α-helix	84-121	38
α-helix	123-125	3
α-helix	126-136	11
α-helix	138-155	18

Chain C: 23 helices, 36 β-strands

Element	Residues	Length	Sheet
β-strand	25-31	7	1
β-strand	34-38	5	1
β-strand	47-51	5	1
β-strand	56-64	9	1
β-strand	67-72	6	1
β-strand	80	1	14
β-strand	84-91	8	1
β-strand	93-96	4	15
β-strand	104-105	2	16
α-helix	112-118	7
β-strand	123	1	17
β-strand	139-143	5	18
β-strand	151-153	3	19
β-strand	157-162	6	18
β-strand	170-173	4	18
β-strand	179-185	7	19
α-helix	186-187	2
β-strand	189-191	3	18
β-strand	198-202	5	19
β-strand	205-209	5	19
β-strand	213-216	4	15
α-helix	220-222	3
β-strand	225-227	3	16
β-strand	232	1	20
α-helix	238-243	6
β-strand	247	1	20
β-strand	253-255	3	16
α-helix	263-272	10
β-strand	277-285	9	16
α-helix	287-296	10
α-helix	297-299	3
β-strand	302-303	2	21
β-strand	308-309	2	21
α-helix	311-314	4
β-strand	315-321	7	16
α-helix	326-345	20
β-strand	349-354	6	16
α-helix	357-370	14
β-strand	377	1	22
β-strand	380	1	22
α-helix	384-392	9
β-strand	396-399	4	16
α-helix	400	1
β-strand	407-416	10	16
α-helix	426-431	6
β-strand	437-438	2	23
β-strand	441	1	24
α-helix	443-448	6
β-strand	454	1	24
β-strand	460-461	2	23
α-helix	464-472	9
α-helix	478-502	25
α-helix	509-520	12
α-helix	521-525	5
α-helix	540-562	23
α-helix	567-583	17
α-helix	584-586	3
α-helix	589-591	3
α-helix	593-615	23

Chain d: 3 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	2-24	23
α-helix	30-52	23
α-helix	59-61	3
β-strand	63	1	77

Chain D: 22 helices, 32 β-strands

Element	Residues	Length	Sheet
α-helix	10-19	10
β-strand	26-28	3	1
β-strand	31-35	5	1
β-strand	38-41	4	1
α-helix	47	1
β-strand	48	1	14
β-strand	52-56	5	1
β-strand	62-71	10	1
β-strand	74-79	6	1
β-strand	87	1	25
β-strand	92-95	4	1
β-strand	101-104	4	50
α-helix	106-108	3
β-strand	111-113	3	51
β-strand	119	1	51
α-helix	124-126	3
β-strand	130-133	4	50
β-strand	139	1	17
α-helix	141-143	3
β-strand	150	1	52
β-strand	151-152	2	53
α-helix	156-159	4
β-strand	165	1	52
β-strand	169	1	51
β-strand	172-174	3	54
α-helix	180-190	11
β-strand	192-193	2	53
β-strand	208-213	6	51
β-strand	217	1	55
α-helix	219-232	14
α-helix	234-237	4
β-strand	238-241	4	51
β-strand	244	1	55
α-helix	249-270	22
β-strand	273-278	6	51
α-helix	281-293	13
α-helix	301-303	3
α-helix	308-316	9
β-strand	328-333	6	51
β-strand	334-336	3	54
α-helix	345-352	8
β-strand	356-357	2	56
β-strand	358-359	2	54
β-strand	360	1	57
α-helix	362-366	5
β-strand	373	1	57
β-strand	379-380	2	56
α-helix	381-385	5
α-helix	396-420	25
α-helix	427-439	13
α-helix	440-444	5
α-helix	454-465	12
α-helix	470-473	4
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	P17255 (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

>9ODU_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

>9ODU_2 V-type proton ATPase subunit E (chains G, I, K)
MSSAITALTPNQVNDELNKMQAFIRKEAEEKAKEIQLKADQEYEIEKTNIVRNETNNIDG
NFKSKLKKAMLSQQITKSTIANKMRLKVLSAREQSLDGIFEETKEKLSGIANNRDEYKPI
LQSLIVEALLKLLEPKAIVKALERDVDLIESMKDDIMREYGEKAQRAPLEEIVISNDYLN
KDLVSGGVVVSNASDKIEINNTLEERLKLLSEEALPAIRLELYGPSKTRKFFD

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

>9ODU_3 V-type proton ATPase subunit G (chains H, J, L)
MSQKNGIATLLQAEKEAHEIVSKARKYRQDKLKQAKTDAAKEIDSYKIQKDKELKEFEQK
NAGGVGELEKKAEAGVQGELAEIKKIAEKKKDDVVKILIETVIKPSAEVHINAL

Sequence of entity 4 (M), FASTA

>9ODU_4 V-type proton ATPase subunit D (chains M)
MSGNREQVFPTRMTLGLMKTKLKGANQGYSLLKRKSEALTKRFRDITKRIDDAKQKMGRV
MQTAAFSLAEVSYATGENIGYQVQESVSTARFKVRARQENVSGVYLSQFESYIDPEINDF
RLTGLGRGGQQVQRAKEIYSRAVETLVELASLQTAFIILDEVIKVTNRRVNAIEHVIIPR
TENTIAYINSELDELDREEFYRLKKVQEKKQNETAKLDAEMKLKRDRAEQDASEVAADEE
PQGETLVADQEDDVIF

Sequence of entity 5 (N), FASTA

>9ODU_5 V-type proton ATPase subunit F (chains N)
MAEKRTLIAVIADEDTTTGLLLAGIGQITPETQEKNFFVYQEGKTTKEEITDKFNHFTEE
RDDIAILLINQHIAENIRARVDSFTNAFPAILEIPSKDHPYDPEKDSVLKRVRKLFGE

Sequence of entity 6 (O), FASTA

>9ODU_6 V-type proton ATPase subunit C (chains O)
MATALYTANDFILISLPQNAQPVTAPGSKTDSWFNETLIGGRAFVSDFKIPEFKIGSLDT
LIVESEELSKVDNQIGASIGKIIEILQGLNETSTNAYRTLPINNMPVPEYLENFQWQTRK
FKLDKSIKDLITLISNESSQLDADVRATYANYNSAKTNLAAAERKKTGDLSVRSLHDIVK
PEDFVLNSEHLTTVLVAVPKSLKSDFEKSYETLSKNVVPASASVIAEDAEYVLFNVHLFK
KNVQEFTTAAREKKFIPREFNYSEELIDQLKKEHDSAASLEQSLRVQLVRLAKTAYVDVF
INWFHIKALRVYVESVLRYGLPPHFNIKIIAVPPKNLSKCKSELIDAFGFLGGNAFMKDK
KGKINKQDTSLHQYASLVDTEYEPFVMYIINL

Sequence of entity 7 (R), FASTA

>9ODU_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

>9ODU_8 V-type proton ATPase subunit d (chains S)
MEGVYFNIDNGFIEGVVRGYRNGLLSNNQYINLTQCDTLEDLKLQLSSTDYGNFLSSVSS
ESLTTSLIQEYASSKLYHEFNYIRDQSSGSTRKFMDYITYGYMIDNVALMITGTIHDRDK
GEILQRCHPLGWFDTLPTLSVATDLESLYETVLVDTPLAPYFKNCFDTAEELDDMNIEII
RNKLYKAYLEDFYNFVTEEIPEPAKECMQTLLGFEADRRSINIALNSLQSSDIDPDLKSD
LLPNIGKLYPLATFHLAQAQDFEGVRAALANVYEYRGFLETGNLEDHFYQLEMELCRDAF
TQQFAISTVWAWMKSKEQEVRNITWIAECIAQNQRERINNYISVY

Sequence of entity 9 (T), FASTA

>9ODU_9 V-type proton ATPase subunit c'' (chains T)
MNKESKDDDMSLGKFSFSHFLYYLVLIVVIVYGLYKLFTGHGSDINFGKFLLRTSPYMWA
NLGIALCVGLSVVGAAWGIFITGSSMIGAGVRAPRITTKNLISIIFCEVVAIYGLIIAIV
FSSKLTVATAENMYSKSNLYTGYSLFWAGITVGASNLICGIAVGITGATAAISDAADSAL
FVKILVIEIFGSILGLLGLIVGLLMAGKASEFQ

Sequence of entity 10 (U), FASTA

>9ODU_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

>9ODU_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

>9ODU_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

Yeast V-ATPase bound to Rtc5p, rotary state 2. Wilkens, S., Khan, M.M. To be published.

Other PDB entries of the same protein (UniProt P17255 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1GPP 1.35 Å, Crystal structure of the S.cerevisiae Homing Endonuclease PI-SceI Domain I
1DFA 2.0 Å, Crystal structure of pi-scei in C2 space group
1EF0 2.1 Å, Crystal structure of pi-scei miniprecursor
1JVA 2.1 Å, Crystal structure of the VMA1-derived endonuclease bearing the N and C extein propeptides
1VDE 2.4 Å, Pi-scei, a homing endonuclease with protein splicing activity
9COP 2.7 Å, Yeast RAVE bound to V-ATPase V1 complex
1UM2 2.9 Å, Crystal Structure of the Vma1-Derived Endonuclease with the Ligated Extein Segment
1LWT 3.2 Å, Crystal structure of the intein homing endonuclease PI-SceI bound to its substrate DNA…
7TMO 3.3 Å, V1 complex lacking subunit C from Saccharomyces cerevisiae, State 1
7TMP 3.3 Å, V1 complex lacking subunit C from Saccharomyces cerevisiae, State 2
7TMQ 3.3 Å, V1 complex lacking subunit C from Saccharomyces cerevisiae, State 3
1LWS 3.5 Å, Crystal structure of the intein homing endonuclease PI-SceI bound to its recognition…

Browse structure collections

About this viewer

MolViewer shows 9ODU directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.