7TAO: Bafilomycin A1

Cryo-EM structure of bafilomycin A1 bound to yeast VO V-ATPase. Determined by electron microscopy at 3.2 Å resolution. Released 23 Feb 2022.

Method: Electron microscopy
Resolution: 3.2 Å
Organism: Saccharomyces cerevisiae
Chains: 15
Atoms: 22,497
Mol. weight: 359.02 kDa
Ligands: WEV
Released: 23 Feb 2022

Explore 7TAO in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7TAO contains 130 α-helices and 25 β-strands across 15 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, 20 β-strands

Element	Residues	Length	Sheet
α-helix	11-13	3
β-strand	14-22	9	4
α-helix	23-25	3
α-helix	26-36	11
β-strand	40-41	2	4
α-helix	56-78	23
α-helix	82-85	4
α-helix	88-91	4
α-helix	100-103	4
α-helix	104-145	42
α-helix	149-152	4
β-strand	186	1	5
β-strand	189-192	4	6
α-helix	193-207	15
β-strand	214-215	2	6
α-helix	221	1
β-strand	222-224	3	7
β-strand	229-231	3	7
β-strand	233-237	5	6
β-strand	239	1	5
α-helix	243-255	13
β-strand	259-260	2	6
α-helix	267-276	10
α-helix	280-303	24
α-helix	306-323	18
β-strand	327-328	2	4
β-strand	334-342	9	4
α-helix	343-345	3
α-helix	346-360	15
β-strand	368-371	4	4
β-strand	379	1	8
α-helix	388-397	10
α-helix	399-401	3
α-helix	404-406	3
α-helix	408-423	16
α-helix	426-441	16
α-helix	443-448	6
α-helix	453-456	4
α-helix	462-479	18
β-strand	482	1	9
β-strand	485	1	9
β-strand	494-495	2	10
β-strand	506-507	2	1
β-strand	509-510	2	10
α-helix	520-522	3
α-helix	528-562	35
α-helix	565-567	3
α-helix	568-572	5
α-helix	573-582	10
α-helix	584-594	11
α-helix	598-601	4
α-helix	603-606	4
α-helix	608-617	10
α-helix	630-657	28
α-helix	707-732	26
α-helix	735-760	26
α-helix	763-780	18
α-helix	781-788	8
α-helix	789-799	11
α-helix	800-805	6
α-helix	806-809	4
α-helix	814-815	2
β-strand	816	1	8

Chain B: 22 helices, 0 β-strands

Element	Residues	Length
α-helix	6-9	4
α-helix	11-22	12
α-helix	27-34	8
α-helix	39-48	10
α-helix	65-85	21
α-helix	90-116	27
α-helix	120-126	7
α-helix	137-140	4
α-helix	145-148	4
α-helix	149-153	5
α-helix	159-161	3
α-helix	165-167	3
α-helix	174-198	25
α-helix	201	1
α-helix	204-228	25
α-helix	237-240	4
α-helix	251-258	8
α-helix	262-269	8
α-helix	276-280	5
α-helix	284-299	16
α-helix	307-332	26
α-helix	335-337	3

Chain C: 9 helices, 0 β-strands

Element	Residues	Length
α-helix	17-38	22
α-helix	42-44	3
α-helix	47-53	7
α-helix	56-90	35
α-helix	96-122	27
α-helix	136-176	41
α-helix	178-180	3
α-helix	181-205	25
α-helix	210-212	3

Chain D: 6 helices, 0 β-strands

Element	Residues	Length
α-helix	15-51	37
α-helix	53-56	4
α-helix	61-82	22
α-helix	92-127	36
α-helix	131-133	3
α-helix	134-163	30

Chain E: 5 helices, 0 β-strands

Element	Residues	Length
α-helix	10-43	34
α-helix	48-50	3
α-helix	55-77	23
α-helix	84-118	35
α-helix	125-152	28

Chain F: 5 helices, 0 β-strands

Element	Residues	Length
α-helix	9-42	34
α-helix	50-53	4
α-helix	55-75	21
α-helix	84-119	36
α-helix	125-151	27

Chain G: 5 helices, 0 β-strands

Element	Residues	Length
α-helix	9-45	37
α-helix	55-77	23
α-helix	84-117	34
α-helix	119-121	3
α-helix	124-152	29

Chain H: 6 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	2	1	3
β-strand	5	1	3
α-helix	9-45	37
α-helix	55-60	6
α-helix	63-75	13
α-helix	84-121	38
α-helix	123-125	3
α-helix	126-152	27

7 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 c'	D	protein	164	Saccharomyces cerevisiae	P32842 (AlphaFold model)
V-type proton ATPase subunit c''	C	protein	213	Saccharomyces cerevisiae	P23968 (AlphaFold model)
V0 assembly protein 1	N	protein	265	Saccharomyces cerevisiae	P53262 (AlphaFold model)
V-type proton ATPase subunit e	M	protein	73	Saccharomyces cerevisiae	Q3E7B6 (AlphaFold model)
V-type proton ATPase subunit c	E, F, G, H, I, J, K, L	protein	160	Saccharomyces cerevisiae	P25515
Yeast V-ATPase subunit f	O	protein	85	Saccharomyces cerevisiae	P0C5R9
V-type proton ATPase subunit d	B	protein	345	Saccharomyces cerevisiae	P32366
V-type proton ATPase subunit a, vacuolar isoform	A	protein	840	Saccharomyces cerevisiae	P32563

Sequence of entity 1 (D), FASTA

>7TAO_1 V-type proton ATPase subunit c' (chains D)
MSTQLASNIYAPLYAPFFGFAGCAAAMVLSCLGAAIGTAKSGIGIAGIGTFKPELIMKSL
IPVVMSGILAIYGLVVAVLIAGNLSPTEDYTLFNGFMHLSCGLCVGFACLSSGYAIGMVG
DVGVRKYMHQPRLFVGIVLILIFSEVLGLYGMIVALILNTRGSE

Sequence of entity 2 (C), FASTA

>7TAO_2 V-type proton ATPase subunit c'' (chains C)
MNKESKDDDMSLGKFSFSHFLYYLVLIVVIVYGLYKLFTGHGSDINFGKFLLRTSPYMWA
NLGIALCVGLSVVGAAWGIFITGSSMIGAGVRAPRITTKNLISIIFCEVVAIYGLIIAIV
FSSKLTVATAENMYSKSNLYTGYSLFWAGITVGASNLICGIAVGITGATAAISDAADSAL
FVKILVIEIFGSILGLLGLIVGLLMAGKASEFQ

Sequence of entity 3 (N), FASTA

>7TAO_3 V0 assembly protein 1 (chains N)
MVFGQLYALFIFTLSCCISKTVQADSSKESSSFISFDKESNWDTISTISSTADVISSVDS
AIAVFEFDNFSLLDNLMIDEEYPFFNRFFANDVSLTVHDDSPLNISQSLSPIMEQFTVDE
LPESASDLLYEYSLDDKSIVLFKFTSDAYDLKKLDEFIDSCLSFLEDKSGDNLTVVINSL
GWAFEDEDGDDEYATEETLSHHDNNKGKEGDDDILSSIWTEGLLMCLIVSALLLFILIVA
LSWISNLDITYGALEKSTNPIKKNN

Sequence of entity 4 (M), FASTA

>7TAO_4 V-type proton ATPase subunit e (chains M)
MSSFYTVVGVFIVVSAMSVLFWIMAPKNNQAVWRSTVILTLAMMFLMWAITFLCQLHPLV
APRRSDLRPEFAE

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

>7TAO_5 V-type proton ATPase subunit c (chains E, F, G, H, I, J, K, L)
MTELCPVYAPFFGAIGCASAIIFTSLGAAYGTAKSGVGICATCVLRPDLLFKNIVPVIMA
GIIAIYGLVVSVLVCYSLGQKQALYTGFIQLGAGLSVGLSGLAAGFAIGIVGDAGVRGSS
QQPRLFVGMILILIFAEVLGLYGLIVALLLNSRATQDVVC

Sequence of entity 6 (O), FASTA

>7TAO_6 Yeast V-ATPase subunit f (chains O)
MRPVVSTGKAWCCTVLSAFGVVILSVIAHLFNTNHESFVGSINDPEDGPAVAHTVYLAAL
VYLVFFVFCGFQVYLARRKPSIELR

Sequence of entity 7 (B), FASTA

>7TAO_7 V-type proton ATPase subunit d (chains B)
MEGVYFNIDNGFIEGVVRGYRNGLLSNNQYINLTQCDTLEDLKLQLSSTDYGNFLSSVSS
ESLTTSLIQEYASSKLYHEFNYIRDQSSGSTRKFMDYITYGYMIDNVALMITGTIHDRDK
GEILQRCHPLGWFDTLPTLSVATDLESLYETVLVDTPLAPYFKNCFDTAEELDDMNIEII
RNKLYKAYLEDFYNFVTEEIPEPAKECMQTLLGFEADRRSINIALNSLQSSDIDPDLKSD
LLPNIGKLYPLATFHLAQAQDFEGVRAALANVYEYRGFLETGNLEDHFYQLEMELCRDAF
TQQFAISTVWAWMKSKEQEVRNITWIAECIAQNQRERINNYISVY

Sequence of entity 8 (A), FASTA

>7TAO_8 V-type proton ATPase subunit a, vacuolar isoform (chains A)
MAEKEEAIFRSAEMALVQFYIPQEISRDSAYTLGQLGLVQFRDLNSKVRAFQRTFVNEIR
RLDNVERQYRYFYSLLKKHDIKLYEGDTDKYLDGSGELYVPPSGSVIDDYVRNASYLEER
LIQMEDATDQIEVQKNDLEQYRFILQSGDEFFLKGDNTDSTSYMDEDMIDANGENIAAAI
GASVNYVTGVIARDKVATLEQILWRVLRGNLFFKTVEIEQPVYDVKTREYKHKNAFIVFS
HGDLIIKRIRKIAESLDANLYDVDSSNEGRSQQLAKVNKNLSDLYTVLKTTSTTLESELY
AIAKELDSWFQDVTREKAIFEILNKSNYDTNRKILIAEGWIPRDELATLQARLGEMIARL
GIDVPSIIQVLDTNHTPPTFHRTNKFTAGFQSICDCYGIAQYREINAGLPTIVTFPFMFA
IMFGDMGHGFLMTLAALSLVLNEKKINKMKRGEIFDMAFTGRYIILLMGVFSMYTGFLYN
DIFSKTMTIFKSGWKWPDHWKKGESITATSVGTYPIGLDWAWHGTENALLFSNSYKMKLS
ILMGFIHMTYSYFFSLANHLYFNSMIDIIGNFIPGLLFMQGIFGYLSVCIVYKWAVDWVK
DGKPAPGLLNMLINMFLSPGTIDDELYPHQAKVQVFLLLMALVCIPWLLLVKPLHFKFTH
KKKSHEPLPSTEADASSEDLEAQQLISAMDADDAEEEEVGSGSHGEDFGDIMIHQVIHTI
EFCLNCVSHTASYLRLWALSLAHAQLSSVLWTMTIQIAFGFRGFVGVFMTVALFAMWFAL
TCAVLVLMEGTSAMLHSLRLHWVESMSKFFVGEGLPYEPFAFEYKDMEVAVASASSSASS

Ligands and cofactors

ID	Name	Formula	Copies
WEV	(5R)-2,4-dideoxy-1-C-{(2S,3R,4S)-3-hydroxy-4-[(2R,3S,4E,6E,9R,10S,11R,12E,14Z)-…	C35 H58 O9	9

Primary citation

Cryo-EM of the Yeast V O Complex Reveals Distinct Binding Sites for Macrolide V-ATPase Inhibitors. Keon, K.A., Benlekbir, S., Kirsch, S.H. et al. ACS Chem Biol (2022) 17:619-628. DOI 10.1021/acschembio.1c00894 · PubMed

Other PDB entries of the same protein (UniProt P32842 (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
9E7L 3.33 Å, Yeast V-ATPase Vo proton channel bound to nanobody 2WVA7
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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