9E7L: Yeast V-ATPase Vo proton channel

Yeast V-ATPase Vo proton channel bound to nanobody 2WVA7. Determined by electron microscopy at 3.33 Å resolution. Released 5 Feb 2025.

Method: Electron microscopy
Resolution: 3.33 Å
Organisms: Saccharomyces cerevisiae, Lama glama
Chains: 23
Atoms: 29,192
Mol. weight: 472.75 kDa
Released: 5 Feb 2025

Explore 9E7L in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9E7L contains 150 α-helices and 126 β-strands across 23 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: 43 helices, 18 β-strands

Element	Residues	Length	Sheet
α-helix	11-13	3
β-strand	14-22	9	29
α-helix	23-36	14
β-strand	40-41	2	29
α-helix	50-52	3
α-helix	56-78	23
α-helix	83-85	3
α-helix	100-103	4
α-helix	104-145	42
α-helix	149-152	4
β-strand	186-192	7	30
α-helix	196-206	11
β-strand	213-217	5	30
β-strand	222-224	3	31
β-strand	229-231	3	31
β-strand	233-239	7	30
α-helix	243-255	13
β-strand	259-260	2	30
α-helix	267-323	57
β-strand	327-328	2	29
β-strand	334-342	9	29
α-helix	343-345	3
α-helix	346-360	15
β-strand	368-371	4	29
α-helix	376-378	3
β-strand	379	1	32
α-helix	387-395	9
α-helix	399-401	3
α-helix	405-406	2
α-helix	408-420	13
α-helix	426-441	16
α-helix	443-446	4
α-helix	453-460	8
α-helix	462-478	17
β-strand	482	1	33
β-strand	485	1	33
α-helix	491-492	2
β-strand	494-495	2	34
β-strand	506-507	2	10
β-strand	509-510	2	34
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	585-593	9
α-helix	598-601	4
α-helix	604-607	4
α-helix	608-617	10
α-helix	630-657	28
α-helix	708-732	25
α-helix	735-754	20
α-helix	758-760	3
α-helix	763-782	20
α-helix	783-788	6
α-helix	789-799	11
α-helix	800-805	6
α-helix	806-808	3
β-strand	816	1	32
α-helix	827-831	5

Chain B: 24 helices, 0 β-strands

Element	Residues	Length
α-helix	7-21	15
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	120-124	5
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	200-201	2
α-helix	204-227	24
α-helix	235-238	4
α-helix	239-241	3
α-helix	251-258	8
α-helix	262-269	8
α-helix	273-275	3
α-helix	284-299	16
α-helix	307-332	26
α-helix	335-337	3

Chain C: 8 helices, 0 β-strands

Element	Residues	Length
α-helix	17-38	22
α-helix	47-53	7
α-helix	56-89	34
α-helix	96-99	4
α-helix	101-122	22
α-helix	130-132	3
α-helix	136-174	39
α-helix	178-207	30

Chain D: 6 helices, 0 β-strands

Element	Residues	Length
α-helix	16-47	32
α-helix	53-55	3
α-helix	61-81	21
α-helix	92-125	34
α-helix	131-133	3
α-helix	134-162	29

Chain E: 4 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	10-43	34
α-helix	55-75	21
α-helix	84-119	36
α-helix	125-153	29
β-strand	159	1	18

Chain F: 5 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	10-42	33
α-helix	47-49	3
α-helix	55-75	21
α-helix	84-119	36
α-helix	125-154	30
β-strand	159	1	4

Chain G: 6 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	10-42	33
α-helix	47-49	3
α-helix	50-53	4
α-helix	55-75	21
α-helix	84-119	36
α-helix	125-153	29
β-strand	159	1	5

Chain H: 7 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	9-42	34
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	126-154	29
β-strand	159	1	6

12 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)
Nanobody 2WVA7	Q, R, S, T, U, V, W, X	protein	136	Lama glama
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
V-type proton ATPase subunit a, vacuolar isoform	A	protein	840	Saccharomyces cerevisiae	P32563

Sequence of entity 1 (B), FASTA

>9E7L_1 V-type proton ATPase subunit d (chains B)
MEGVYFNIDNGFIEGVVRGYRNGLLSNNQYINLTQCDTLEDLKLQLSSTDYGNFLSSVSS
ESLTTSLIQEYASSKLYHEFNYIRDQSSGSTRKFMDYITYGYMIDNVALMITGTIHDRDK
GEILQRCHPLGWFDTLPTLSVATDLESLYETVLVDTPLAPYFKNCFDTAEELDDMNIEII
RNKLYKAYLEDFYNFVTEEIPEPAKECMQTLLGFEADRRSINIALNSLQSSDIDPDLKSD
LLPNIGKLYPLATFHLAQAQDFEGVRAALANVYEYRGFLETGNLEDHFYQLEMELCRDAF
TQQFAISTVWAWMKSKEQEVRNITWIAECIAQNQRERINNYISVY

Sequence of entity 2 (C), FASTA

>9E7L_2 V-type proton ATPase subunit c'' (chains C)
MNKESKDDDMSLGKFSFSHFLYYLVLIVVIVYGLYKLFTGHGSDINFGKFLLRTSPYMWA
NLGIALCVGLSVVGAAWGIFITGSSMIGAGVRAPRITTKNLISIIFCEVVAIYGLIIAIV
FSSKLTVATAENMYSKSNLYTGYSLFWAGITVGASNLICGIAVGITGATAAISDAADSAL
FVKILVIEIFGSILGLLGLIVGLLMAGKASEFQ

Sequence of entity 3 (D), FASTA

>9E7L_3 V-type proton ATPase subunit c' (chains D)
MSTQLASNIYAPLYAPFFGFAGCAAAMVLSCLGAAIGTAKSGIGIAGIGTFKPELIMKSL
IPVVMSGILAIYGLVVAVLIAGNLSPTEDYTLFNGFMHLSCGLCVGFACLSSGYAIGMVG
DVGVRKYMHQPRLFVGIVLILIFSEVLGLYGMIVALILNTRGSE

Sequence of entity 4 (Q, R, S, T, U, V, W, X), FASTA

>9E7L_4 Nanobody 2WVA7 (chains Q, R, S, T, U, V, W, X)
QVQLQESGGGLVEIGGSLRLSCAASGTLFTFNTMAWYRQAPGKQREFIATITSGGNTNYA
DSVQGRFTISRGNAKNTLYLQMNSLKPEDTAVYYCNARTMTGPFDYWGQGTQVTVSSAAA
YPYDVPDYGSHHHHHH

Sequence of entity 5 (E, F, G, H, I, J, K, L), FASTA

>9E7L_5 V-type proton ATPase subunit c (chains E, F, G, H, I, J, K, L)
MTELCPVYAPFFGAIGCASAIIFTSLGAAYGTAKSGVGICATCVLRPDLLFKNIVPVIMA
GIIAIYGLVVSVLVCYSLGQKQALYTGFIQLGAGLSVGLSGLAAGFAIGIVGDAGVRGSS
QQPRLFVGMILILIFAEVLGLYGLIVALLLNSRATQDVVC

Sequence of entity 6 (M), FASTA

>9E7L_6 V-type proton ATPase subunit e (chains M)
MSSFYTVVGVFIVVSAMSVLFWIMAPKNNQAVWRSTVILTLAMMFLMWAITFLCQLHPLV
APRRSDLRPEFAE

Sequence of entity 7 (N), FASTA

>9E7L_7 V0 assembly protein 1 (chains N)
MVFGQLYALFIFTLSCCISKTVQADSSKESSSFISFDKESNWDTISTISSTADVISSVDS
AIAVFEFDNFSLLDNLMIDEEYPFFNRFFANDVSLTVHDDSPLNISQSLSPIMEQFTVDE
LPESASDLLYEYSLDDKSIVLFKFTSDAYDLKKLDEFIDSCLSFLEDKSGDNLTVVINSL
GWAFEDEDGDDEYATEETLSHHDNNKGKEGDDDILSSIWTEGLLMCLIVSALLLFILIVA
LSWISNLDITYGALEKSTNPIKKNN

Sequence of entity 8 (O), FASTA

>9E7L_8 Yeast V-ATPase subunit f (chains O)
MRPVVSTGKAWCCTVLSAFGVVILSVIAHLFNTNHESFVGSINDPEDGPAVAHTVYLAAL
VYLVFFVFCGFQVYLARRKPSIELR

Sequence of entity 9 (A), FASTA

>9E7L_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
9E76 3.4 Å, Yeast V-ATPase Vo proton channel bound to nanobody 1WVA25
6C6L 3.5 Å, Yeast Vacuolar ATPase Vo in lipid nanodisc

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