6O7T: Saccharomyces cerevisiae V-ATPase Vph1-VO

Saccharomyces cerevisiae V-ATPase Vph1-VO. Determined by electron microscopy at 3.2 Å resolution. Released 3 Apr 2019.

Method: Electron microscopy
Resolution: 3.2 Å
Organism: Saccharomyces cerevisiae
Chains: 15
Atoms: 19,730
Mol. weight: 356.14 kDa
Released: 3 Apr 2019

Explore 6O7T in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6O7T contains 113 α-helices and 21 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: 34 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	14-19	6	1
β-strand	20-22	3	2
α-helix	29-34	6
β-strand	40-41	2	1
α-helix	56-58	3
α-helix	60-78	19
α-helix	88-92	5
α-helix	106-144	39
β-strand	187-191	5	3
α-helix	196-206	11
β-strand	212-217	6	3
β-strand	222	1	4
β-strand	231	1	4
β-strand	234-239	6	3
α-helix	243-255	13
β-strand	261	1	3
α-helix	267-303	37
α-helix	308-324	17
β-strand	327-328	2	2
β-strand	334-336	3	2
β-strand	339-342	4	1
α-helix	343-345	3
α-helix	346-358	13
β-strand	368-370	3	1
β-strand	379	1	5
α-helix	388-391	4
α-helix	404-406	3
α-helix	411-423	13
α-helix	426-441	16
α-helix	453-460	8
α-helix	463-478	16
β-strand	482	1	6
β-strand	485	1	6
β-strand	494-495	2	7
β-strand	506-507	2	8
β-strand	509-510	2	7
α-helix	520-522	3
α-helix	528-559	32
α-helix	565-567	3
α-helix	568-572	5
α-helix	573-579	7
α-helix	580-584	5
α-helix	585-594	10
α-helix	603-605	3
α-helix	608-612	5
α-helix	631-654	24
α-helix	710-729	20
α-helix	731-733	3
α-helix	735-752	18
α-helix	756-758	3
α-helix	766-781	16
α-helix	782-789	8
α-helix	790-802	13
β-strand	816	1	5

Chain b: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	221-249	29

Chain c: 8 helices, 0 β-strands

Element	Residues	Length
α-helix	25-38	14
α-helix	42-44	3
α-helix	47-53	7
α-helix	56-88	33
α-helix	94-96	3
α-helix	105-122	18
α-helix	136-167	32
α-helix	181-205	25

Chain d: 13 helices, 0 β-strands

Element	Residues	Length
α-helix	11-20	10
α-helix	28-31	4
α-helix	39-46	8
α-helix	65-84	20
α-helix	92-114	23
α-helix	120-126	7
α-helix	145-151	7
α-helix	177-193	17
α-helix	202-227	26
α-helix	252-257	6
α-helix	262-268	7
α-helix	288-297	10
α-helix	307-331	25

Chain e: 2 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	5-23	19
α-helix	30-53	24
β-strand	63-64	2	8

Chain f: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	12-32	21
α-helix	48-69	22

Chain g: 5 helices, 0 β-strands

Element	Residues	Length
α-helix	9-42	34
α-helix	47-49	3
α-helix	55-75	21
α-helix	84-118	35
α-helix	125-151	27

Chain h: 5 helices, 0 β-strands

Element	Residues	Length
α-helix	9-41	33
α-helix	55-73	19
α-helix	84-118	35
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 a, vacuolar isoform	a	protein	862	Saccharomyces cerevisiae	P32563 (AlphaFold model)
V0 assembly protein 1	b	protein	265	Saccharomyces cerevisiae	P53262 (AlphaFold model)
V-type proton ATPase subunit c''	c	protein	213	Saccharomyces cerevisiae	P23968 (AlphaFold model)
V-type proton ATPase subunit d	d	protein	345	Saccharomyces cerevisiae	P32366 (AlphaFold model)
Putative protein YPR170W-B	f	protein	85	Saccharomyces cerevisiae	P0C5R9
V-type proton ATPase subunit c	g, h, i, j, k, l, m, n	protein	160	Saccharomyces cerevisiae	P25515
V-type proton ATPase subunit c'	o	protein	164	Saccharomyces cerevisiae	P32842
V-type proton ATPase subunit e	e	protein	73	Saccharomyces cerevisiae	Q3E7B6

Sequence of entity 1 (a), FASTA

>6O7T_1 V-type proton ATPase subunit a, vacuolar isoform (chains a)
MAEKEEAIFRSAEMALVQFYIPQEISRDSAYTLGQLGLVQFRDLNSKVRAFQRTFVNEIR
RLDNVERQYRYFYSLLKKHDIKLYEGDTDKYLDGSGELYVPPSGSVIDDYVRNASYLEER
LIQMEDATDQIEVQKNDLEQYRFILQSGDEFFLKGDNTDSTSYMDEDMIDANGENIAAAI
GASVNYVTGVIARDKVATLEQILWRVLRGNLFFKTVEIEQPVYDVKTREYKHKNAFIVFS
HGDLIIKRIRKIAESLDANLYDVDSSNEGRSQQLAKVNKNLSDLYTVLKTTSTTLESELY
AIAKELDSWFQDVTREKAIFEILNKSNYDTNRKILIAEGWIPRDELATLQARLGEMIARL
GIDVPSIIQVLDTNHTPPTFHRTNKFTAGFQSICDCYGIAQYREINAGLPTIVTFPFMFA
IMFGDMGHGFLMTLAALSLVLNEKKINKMKRGEIFDMAFTGRYIILLMGVFSMYTGFLYN
DIFSKTMTIFKSGWKWPDHWKKGESITATSVGTYPIGLDWAWHGTENALLFSNSYKMKLS
ILMGFIHMTYSYFFSLANHLYFNSMIDIIGNFIPGLLFMQGIFGYLSVCIVYKWAVDWVK
DGKPAPGLLNMLINMFLSPGTIDDELYPHQAKVQVFLLLMALVCIPWLLLVKPLHFKFTH
KKKSHEPLPSTEADASSEDLEAQQLISAMDADDAEEEEVGSGSHGEDFGDIMIHQVIHTI
EFCLNCVSHTASYLRLWALSLAHAQLSSVLWTMTIQIAFGFRGFVGVFMTVALFAMWFAL
TCAVLVLMEGTSAMLHSLRLHWVESMSKFFVGEGLPYEPFAFEYKDMEVAVASASSSASS
DYKDHDGDYKDHDIDYKDDDDK

Sequence of entity 2 (b), FASTA

>6O7T_2 V0 assembly protein 1 (chains b)
MVFGQLYALFIFTLSCCISKTVQADSSKESSSFISFDKESNWDTISTISSTADVISSVDS
AIAVFEFDNFSLLDNLMIDEEYPFFNRFFANDVSLTVHDDSPLNISQSLSPIMEQFTVDE
LPESASDLLYEYSLDDKSIVLFKFTSDAYDLKKLDEFIDSCLSFLEDKSGDNLTVVINSL
GWAFEDEDGDDEYATEETLSHHDNNKGKEGDDDILSSIWTEGLLMCLIVSALLLFILIVA
LSWISNLDITYGALEKSTNPIKKNN

Sequence of entity 3 (c), FASTA

>6O7T_3 V-type proton ATPase subunit c'' (chains c)
MNKESKDDDMSLGKFSFSHFLYYLVLIVVIVYGLYKLFTGHGSDINFGKFLLRTSPYMWA
NLGIALCVGLSVVGAAWGIFITGSSMIGAGVRAPRITTKNLISIIFCEVVAIYGLIIAIV
FSSKLTVATAENMYSKSNLYTGYSLFWAGITVGASNLICGIAVGITGATAAISDAADSAL
FVKILVIEIFGSILGLLGLIVGLLMAGKASEFQ

Sequence of entity 4 (d), FASTA

>6O7T_4 V-type proton ATPase subunit d (chains d)
MEGVYFNIDNGFIEGVVRGYRNGLLSNNQYINLTQCDTLEDLKLQLSSTDYGNFLSSVSS
ESLTTSLIQEYASSKLYHEFNYIRDQSSGSTRKFMDYITYGYMIDNVALMITGTIHDRDK
GEILQRCHPLGWFDTLPTLSVATDLESLYETVLVDTPLAPYFKNCFDTAEELDDMNIEII
RNKLYKAYLEDFYNFVTEEIPEPAKECMQTLLGFEADRRSINIALNSLQSSDIDPDLKSD
LLPNIGKLYPLATFHLAQAQDFEGVRAALANVYEYRGFLETGNLEDHFYQLEMELCRDAF
TQQFAISTVWAWMKSKEQEVRNITWIAECIAQNQRERINNYISVY

Sequence of entity 5 (f), FASTA

>6O7T_5 Putative protein YPR170W-B (chains f)
MRPVVSTGKAWCCTVLSAFGVVILSVIAHLFNTNHESFVGSINDPEDGPAVAHTVYLAAL
VYLVFFVFCGFQVYLARRKPSIELR

Sequence of entity 6 (g, h, i, j, k, l, m, n), FASTA

>6O7T_6 V-type proton ATPase subunit c (chains g, h, i, j, k, l, m, n)
MTELCPVYAPFFGAIGCASAIIFTSLGAAYGTAKSGVGICATCVLRPDLLFKNIVPVIMA
GIIAIYGLVVSVLVCYSLGQKQALYTGFIQLGAGLSVGLSGLAAGFAIGIVGDAGVRGSS
QQPRLFVGMILILIFAEVLGLYGLIVALLLNSRATQDVVC

Sequence of entity 7 (o), FASTA

>6O7T_7 V-type proton ATPase subunit c' (chains o)
MSTQLASNIYAPLYAPFFGFAGCAAAMVLSCLGAAIGTAKSGIGIAGIGTFKPELIMKSL
IPVVMSGILAIYGLVVAVLIAGNLSPTEDYTLFNGFMHLSCGLCVGFACLSSGYAIGMVG
DVGVRKYMHQPRLFVGIVLILIFSEVLGLYGMIVALILNTRGSE

Sequence of entity 8 (e), FASTA

>6O7T_8 V-type proton ATPase subunit e (chains e)
MSSFYTVVGVFIVVSAMSVLFWIMAPKNNQAVWRSTVILTLAMMFLMWAITFLCQLHPLV
APRRSDLRPEFAE

Primary citation

Structural comparison of the vacuolar and Golgi V-ATPases fromSaccharomyces cerevisiae. Vasanthakumar, T., Bueler, S.A., Wu, D. et al. Proc Natl Acad Sci U S A (2019) 116:7272-7277. DOI 10.1073/pnas.1814818116 · PubMed

Other PDB entries of the same protein (UniProt P32563 (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
6PE4 3.1 Å, Yeast Vo motor in complex with 1 VopQ molecule
8EAU 3.1 Å, Yeast VO in complex with Vma21p
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
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
7TMR 3.5 Å, V-ATPase from Saccharomyces cerevisiae, State 1
6M0S 3.6 Å, 3.6A Yeast Vo state3 prime

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