9E76: Yeast V-ATPase Vo proton channel

Yeast V-ATPase Vo proton channel bound to nanobody 1WVA25. Determined by electron microscopy at 3.4 Å resolution. Released 5 Feb 2025.

Method: Electron microscopy
Resolution: 3.4 Å
Organisms: Saccharomyces cerevisiae, Lama glama
Chains: 19
Atoms: 26,025
Mol. weight: 418.08 kDa
Released: 5 Feb 2025

Explore 9E76 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9E76 contains 163 α-helices and 75 β-strands across 19 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: 47 helices, 20 β-strands

Element	Residues	Length	Sheet
α-helix	4-6	3
β-strand	10	1	15
α-helix	11-13	3
β-strand	14-22	9	16
α-helix	23-25	3
α-helix	26-36	11
β-strand	40-41	2	16
α-helix	50-52	3
α-helix	56-78	23
α-helix	82-84	3
α-helix	100-103	4
α-helix	104-145	42
α-helix	149-152	4
β-strand	186-192	7	17
α-helix	196-206	11
β-strand	213-217	5	17
β-strand	222-224	3	18
β-strand	229-231	3	18
β-strand	233-239	7	17
α-helix	243-255	13
β-strand	259-261	3	17
α-helix	267-303	37
α-helix	306-323	18
β-strand	327-329	3	16
β-strand	334-342	9	16
α-helix	343-345	3
α-helix	346-360	15
β-strand	368-371	4	16
α-helix	376-378	3
β-strand	379	1	19
α-helix	385-395	11
α-helix	399-401	3
α-helix	404	1
β-strand	405	1	15
α-helix	406	1
α-helix	408-422	15
α-helix	426-441	16
α-helix	443-448	6
α-helix	453-460	8
α-helix	462-478	17
β-strand	482	1	20
β-strand	485	1	20
β-strand	494-495	2	21
β-strand	506-507	2	2
β-strand	509-510	2	21
α-helix	520-522	3
α-helix	528-561	34
α-helix	565-567	3
α-helix	568-572	5
α-helix	573-579	7
α-helix	580-584	5
α-helix	585-595	11
α-helix	598-601	4
α-helix	603-606	4
α-helix	608-617	10
α-helix	630-658	29
α-helix	707-732	26
α-helix	735-753	19
α-helix	755-758	4
α-helix	763-780	18
α-helix	781-789	9
α-helix	790-799	10
α-helix	800-805	6
α-helix	806-808	3
α-helix	814-815	2
β-strand	816	1	19
α-helix	817	1

Chain B: 22 helices, 0 β-strands

Element	Residues	Length
α-helix	3-21	19
α-helix	25-26	2
α-helix	27-34	8
α-helix	39-46	8
α-helix	60-62	3
α-helix	65-85	21
α-helix	89-115	27
α-helix	120-126	7
α-helix	129-131	3
α-helix	136-141	6
α-helix	145-151	7
α-helix	153-155	3
α-helix	159-164	6
α-helix	174-199	26
α-helix	204-227	24
α-helix	235-238	4
α-helix	251-258	8
α-helix	262-270	9
α-helix	273-275	3
α-helix	284-300	17
α-helix	307-332	26
α-helix	338-340	3

Chain C: 11 helices, 0 β-strands

Element	Residues	Length
α-helix	17-38	22
α-helix	42-44	3
α-helix	47-53	7
α-helix	56-89	34
α-helix	96-99	4
α-helix	101-122	22
α-helix	126-129	4
α-helix	130-132	3
α-helix	136-174	39
α-helix	179-205	27
α-helix	209-211	3

Chain D: 6 helices, 0 β-strands

Element	Residues	Length
α-helix	15-47	33
α-helix	53-55	3
α-helix	61-83	23
α-helix	92-127	36
α-helix	131-133	3
α-helix	134-162	29

Chain E: 7 helices, 0 β-strands

Element	Residues	Length
α-helix	10-42	33
α-helix	47-49	3
α-helix	50-53	4
α-helix	55-75	21
α-helix	84-121	38
α-helix	123-125	3
α-helix	126-152	27

Chain F: 7 helices, 0 β-strands

Element	Residues	Length
α-helix	9-42	34
α-helix	47-49	3
α-helix	50-53	4
α-helix	55-75	21
α-helix	84-121	38
α-helix	123-125	3
α-helix	126-152	27

Chain G: 7 helices, 0 β-strands

Element	Residues	Length
α-helix	9-43	35
α-helix	47-49	3
α-helix	50-53	4
α-helix	55-75	21
α-helix	84-119	36
α-helix	123-125	3
α-helix	126-152	27

Chain H: 7 helices, 0 β-strands

Element	Residues	Length
α-helix	10-43	34
α-helix	47-49	3
α-helix	50-53	4
α-helix	55-75	21
α-helix	84-121	38
α-helix	123-125	3
α-helix	126-153	28

11 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 d	B	protein	345	Saccharomyces cerevisiae	P32366 (AlphaFold model)
V-type proton ATPase subunit c''	C	protein	213	Saccharomyces cerevisiae	P23968 (AlphaFold model)
V-type proton ATPase subunit c'	D	protein	164	Saccharomyces cerevisiae	P32842 (AlphaFold model)
V-type proton ATPase subunit c	E, F, G, H, I, J, K, L	protein	160	Saccharomyces cerevisiae	P25515 (AlphaFold model)
V-type proton ATPase subunit e	M	protein	73	Saccharomyces cerevisiae	Q3E7B6
V0 assembly protein 1	N	protein	265	Saccharomyces cerevisiae	P53262
Yeast V-ATPase subunit f	O	protein	85	Saccharomyces cerevisiae	P0C5R9
Nanobody 1WVA25	Q, R, S, T	protein	146	Lama glama
V-type proton ATPase subunit a, vacuolar isoform	A	protein	840	Saccharomyces cerevisiae	P32563

Sequence of entity 1 (B), FASTA

>9E76_1 V-type proton ATPase subunit d (chains B)
MEGVYFNIDNGFIEGVVRGYRNGLLSNNQYINLTQCDTLEDLKLQLSSTDYGNFLSSVSS
ESLTTSLIQEYASSKLYHEFNYIRDQSSGSTRKFMDYITYGYMIDNVALMITGTIHDRDK
GEILQRCHPLGWFDTLPTLSVATDLESLYETVLVDTPLAPYFKNCFDTAEELDDMNIEII
RNKLYKAYLEDFYNFVTEEIPEPAKECMQTLLGFEADRRSINIALNSLQSSDIDPDLKSD
LLPNIGKLYPLATFHLAQAQDFEGVRAALANVYEYRGFLETGNLEDHFYQLEMELCRDAF
TQQFAISTVWAWMKSKEQEVRNITWIAECIAQNQRERINNYISVY

Sequence of entity 2 (C), FASTA

>9E76_2 V-type proton ATPase subunit c'' (chains C)
MNKESKDDDMSLGKFSFSHFLYYLVLIVVIVYGLYKLFTGHGSDINFGKFLLRTSPYMWA
NLGIALCVGLSVVGAAWGIFITGSSMIGAGVRAPRITTKNLISIIFCEVVAIYGLIIAIV
FSSKLTVATAENMYSKSNLYTGYSLFWAGITVGASNLICGIAVGITGATAAISDAADSAL
FVKILVIEIFGSILGLLGLIVGLLMAGKASEFQ

Sequence of entity 3 (D), FASTA

>9E76_3 V-type proton ATPase subunit c' (chains D)
MSTQLASNIYAPLYAPFFGFAGCAAAMVLSCLGAAIGTAKSGIGIAGIGTFKPELIMKSL
IPVVMSGILAIYGLVVAVLIAGNLSPTEDYTLFNGFMHLSCGLCVGFACLSSGYAIGMVG
DVGVRKYMHQPRLFVGIVLILIFSEVLGLYGMIVALILNTRGSE

Sequence of entity 4 (E, F, G, H, I, J, K, L), FASTA

>9E76_4 V-type proton ATPase subunit c (chains E, F, G, H, I, J, K, L)
MTELCPVYAPFFGAIGCASAIIFTSLGAAYGTAKSGVGICATCVLRPDLLFKNIVPVIMA
GIIAIYGLVVSVLVCYSLGQKQALYTGFIQLGAGLSVGLSGLAAGFAIGIVGDAGVRGSS
QQPRLFVGMILILIFAEVLGLYGLIVALLLNSRATQDVVC

Sequence of entity 5 (M), FASTA

>9E76_5 V-type proton ATPase subunit e (chains M)
MSSFYTVVGVFIVVSAMSVLFWIMAPKNNQAVWRSTVILTLAMMFLMWAITFLCQLHPLV
APRRSDLRPEFAE

Sequence of entity 6 (N), FASTA

>9E76_6 V0 assembly protein 1 (chains N)
MVFGQLYALFIFTLSCCISKTVQADSSKESSSFISFDKESNWDTISTISSTADVISSVDS
AIAVFEFDNFSLLDNLMIDEEYPFFNRFFANDVSLTVHDDSPLNISQSLSPIMEQFTVDE
LPESASDLLYEYSLDDKSIVLFKFTSDAYDLKKLDEFIDSCLSFLEDKSGDNLTVVINSL
GWAFEDEDGDDEYATEETLSHHDNNKGKEGDDDILSSIWTEGLLMCLIVSALLLFILIVA
LSWISNLDITYGALEKSTNPIKKNN

Sequence of entity 7 (O), FASTA

>9E76_7 Yeast V-ATPase subunit f (chains O)
MRPVVSTGKAWCCTVLSAFGVVILSVIAHLFNTNHESFVGSINDPEDGPAVAHTVYLAAL
VYLVFFVFCGFQVYLARRKPSIELR

Sequence of entity 8 (Q, R, S, T), FASTA

>9E76_8 Nanobody 1WVA25 (chains Q, R, S, T)
QVQLQESGGGLVQPGGSLRLSCVASGFTFSRYAMTWVRQAPGKGLEWVSDISSGGSSTFY
TDSVKGRFTISRDNAKNTLYLQMNSLKPDDTAIYFCAKGVPSYYSDYERRSKRYDSRGQG
TQVTVSSAAAYPYDVPDYGSHHHHHH

Sequence of entity 9 (A), FASTA

>9E76_9 V-type proton ATPase subunit a, vacuolar isoform (chains A)
MAEKEEAIFRSAEMALVQFYIPQEISRDSAYTLGQLGLVQFRDLNSKVRAFQRTFVNEIR
RLDNVERQYRYFYSLLKKHDIKLYEGDTDKYLDGSGELYVPPSGSVIDDYVRNASYLEER
LIQMEDATDQIEVQKNDLEQYRFILQSGDEFFLKGDNTDSTSYMDEDMIDANGENIAAAI
GASVNYVTGVIARDKVATLEQILWRVLRGNLFFKTVEIEQPVYDVKTREYKHKNAFIVFS
HGDLIIKRIRKIAESLDANLYDVDSSNEGRSQQLAKVNKNLSDLYTVLKTTSTTLESELY
AIAKELDSWFQDVTREKAIFEILNKSNYDTNRKILIAEGWIPRDELATLQARLGEMIARL
GIDVPSIIQVLDTNHTPPTFHRTNKFTAGFQSICDCYGIAQYREINAGLPTIVTFPFMFA
IMFGDMGHGFLMTLAALSLVLNEKKINKMKRGEIFDMAFTGRYIILLMGVFSMYTGFLYN
DIFSKTMTIFKSGWKWPDHWKKGESITATSVGTYPIGLDWAWHGTENALLFSNSYKMKLS
ILMGFIHMTYSYFFSLANHLYFNSMIDIIGNFIPGLLFMQGIFGYLSVCIVYKWAVDWVK
DGKPAPGLLNMLINMFLSPGTIDDELYPHQAKVQVFLLLMALVCIPWLLLVKPLHFKFTH
KKKSHEPLPSTEADASSEDLEAQQLISAMDADDAEEEEVGSGSHGEDFGDIMIHQVIHTI
EFCLNCVSHTASYLRLWALSLAHAQLSSVLWTMTIQIAFGFRGFVGVFMTVALFAMWFAL
TCAVLVLMEGTSAMLHSLRLHWVESMSKFFVGEGLPYEPFAFEYKDMEVAVASASSSASS

Primary citation

Monoclonal nanobodies alter the activity and assembly of the yeast vacuolar H + -ATPase. Knight, K., Park, J.B., Oot, R.A. et al. bioRxiv (2025). DOI 10.1101/2025.01.10.632502 · PubMed

Other PDB entries of the same protein (UniProt P32366 (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
6O7U 3.1 Å, Saccharomyces cerevisiae V-ATPase Stv1-VO
6PE4 3.1 Å, Yeast Vo motor in complex with 1 VopQ molecule
8EAT 3.1 Å, Yeast VO missing subunits a, e, and f in complex with Vma12-22p
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
6C6L 3.5 Å, Yeast Vacuolar ATPase Vo in lipid nanodisc

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