6M0S: 3.6A Yeast Vo state3 prime

3.6A Yeast Vo state3 prime. Determined by electron microscopy at 3.6 Å resolution. Released 4 Nov 2020.

Method: Electron microscopy
Resolution: 3.6 Å
Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Chains: 15
Atoms: 22,042
Mol. weight: 322.87 kDa
Released: 4 Nov 2020

Explore 6M0S in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6M0S contains 136 α-helices and 20 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: 38 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	14-21	8	1
α-helix	26-36	11
β-strand	40-41	2	1
α-helix	45-47	3
α-helix	56-78	23
α-helix	100-103	4
α-helix	104-146	43
α-helix	148-151	4
β-strand	186-192	7	2
α-helix	193-206	14
β-strand	212-217	6	2
β-strand	222	1	3
β-strand	231	1	3
β-strand	233-239	7	2
α-helix	246-255	10
β-strand	258	1	2
β-strand	261	1	2
α-helix	267-306	40
α-helix	308-324	17
β-strand	327-328	2	1
β-strand	335-342	8	1
α-helix	343-345	3
α-helix	346-360	15
β-strand	369-371	3	1
β-strand	379	1	4
α-helix	385-397	13
α-helix	399-401	3
α-helix	410-412	3
α-helix	414-423	10
α-helix	426-441	16
α-helix	443-448	6
α-helix	454-460	7
α-helix	462-479	18
β-strand	482	1	5
β-strand	485	1	5
α-helix	491-492	2
β-strand	506-507	2	6
α-helix	529-562	34
α-helix	566-567	2
α-helix	568-572	5
α-helix	573-579	7
α-helix	583-594	12
α-helix	598-601	4
α-helix	603-607	5
α-helix	609-617	9
α-helix	630-658	29
α-helix	707-725	19
α-helix	728-732	5
α-helix	735-752	18
α-helix	755-758	4
α-helix	763-780	18
α-helix	781-788	8
α-helix	789-799	11
α-helix	800-805	6
β-strand	816	1	4

Chain B: 23 helices, 0 β-strands

Element	Residues	Length
α-helix	12-20	9
α-helix	25-26	2
α-helix	27-34	8
α-helix	39-46	8
α-helix	65-77	13
α-helix	81-85	5
α-helix	90-116	27
α-helix	120-124	5
α-helix	137-140	4
α-helix	145-148	4
α-helix	149-153	5
α-helix	159-161	3
α-helix	174-182	9
α-helix	184-198	15
α-helix	201	1
α-helix	204-215	12
α-helix	217-229	13
α-helix	235-238	4
α-helix	251-257	7
α-helix	262-269	8
α-helix	273-275	3
α-helix	284-296	13
α-helix	308-331	24

Chain C: 10 helices, 0 β-strands

Element	Residues	Length
α-helix	17-35	19
α-helix	42-44	3
α-helix	47-52	6
α-helix	56-89	34
α-helix	94-97	4
α-helix	102-122	21
α-helix	136-176	41
α-helix	178-180	3
α-helix	181-205	25
α-helix	209-212	4

Chain D: 7 helices, 0 β-strands

Element	Residues	Length
α-helix	17-48	32
α-helix	53-55	3
α-helix	57-59	3
α-helix	61-81	21
α-helix	92-125	34
α-helix	131-133	3
α-helix	134-163	30

Chain E: 5 helices, 0 β-strands

Element	Residues	Length
α-helix	10-42	33
α-helix	55-75	21
α-helix	84-119	36
α-helix	123-125	3
α-helix	126-153	28

Chain F: 6 helices, 0 β-strands

Element	Residues	Length
α-helix	10-42	33
α-helix	47-49	3
α-helix	52-54	3
α-helix	55-75	21
α-helix	84-119	36
α-helix	125-151	27

Chain G: 6 helices, 0 β-strands

Element	Residues	Length
α-helix	10-42	33
α-helix	47-49	3
α-helix	55-75	21
α-helix	84-117	34
α-helix	123-125	3
α-helix	126-155	30

Chain H: 6 helices, 0 β-strands

Element	Residues	Length
α-helix	11-42	32
α-helix	47-49	3
α-helix	55-75	21
α-helix	84-119	36
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	825	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P32563 (AlphaFold model)
V-type proton ATPase subunit e	M	protein	71	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Q3E7B6 (AlphaFold model)
Uncharacterized protein YPR170W-B	O	protein	69	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P0C5R9 (AlphaFold model)
V-type proton ATPase subunit d	B	protein	345	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P32366 (AlphaFold model)
V-type proton ATPase subunit c''	C	protein	198	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P23968
V-type proton ATPase subunit c'	D	protein	158	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P32842
V-type proton ATPase subunit c	E, F, G, H, I, J, K, L	protein	159	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P25515
V0 assembly protein 1	N	protein	52	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P53262

Sequence of entity 1 (A), FASTA

>6M0S_1 V-type proton ATPase subunit a, vacuolar isoform (chains A)
EKEEAIFRSAEMALVQFYIPQEISRDSAYTLGQLGLVQFRDLNSKVRAFQRTFVNEIRRL
DNVERQYRYFYSLLKKHDIKLYEGDTDKYLDGSGELYVPPSGSVIDDYVRNASYLEERLI
QMEDATDQIEVQKNDLEQYRFILQSGDEFFLKGDNTDSTSYMDEDMIDANGENIAAAIGA
SVNYVTGVIARDKVATLEQILWRVLRGNLFFKTVEIEQPVYDVKTREYKHKNAFIVFSHG
DLIIKRIRKIAESLDANLYDVDSSNEGRSQQLAKVNKNLSDLYTVLKTTSTTLESELYAI
AKELDSWFQDVTREKAIFEILNKSNYDTNRKILIAEGWIPRDELATLQARLGEMIARLGI
DVPSIIQVLDTNHTPPTFHRTNKFTAGFQSICDCYGIAQYREINAGLPTIVTFPFMFAIM
FGDMGHGFLMTLAALSLVLNEKKINKMKRGEIFDMAFTGRYIILLMGVFSMYTGFLYNDI
FSKTMTIFKSGWKWPDHWKKGESITATSVGTYPIGLDWAWHGTENALLFSNSYKMKLSIL
MGFIHMTYSYFFSLANHLYFNSMIDIIGNFIPGLLFMQGIFGYLSVCIVYKWAVDWVKDG
KPAPGLLNMLINMFLSPGTIDDELYPHQAKVQVFLLLMALVCIPWLLLVKPLHFKFTHKK
KSHEPLPSTEADASSEDLEAQQLISAMDADDAEEEEVGSGSHGEDFGDIMIHQVIHTIEF
CLNCVSHTASYLRLWALSLAHAQLSSVLWTMTIQIAFGFRGFVGVFMTVALFAMWFALTC
AVLVLMEGTSAMLHSLRLHWVESMSKFFVGEGLPYEPFAFEYKDM

Sequence of entity 2 (M), FASTA

>6M0S_2 V-type proton ATPase subunit e (chains M)
MSSFYTVVGVFIVVSAMSVLFWIMAPKNNQAVWRSTVILTLAMMFLMWAITFLCQLHPLV
APRRSDLRPEF

Sequence of entity 3 (O), FASTA

>6M0S_3 Uncharacterized protein YPR170W-B (chains O)
TGKAWCCTVLSAFGVVILSVIAHLFNTNHESFVGSINDPEDGPAVAHTVYLAALVYLVFF
VFCGFQVYL

Sequence of entity 4 (B), FASTA

>6M0S_4 V-type proton ATPase subunit d (chains B)
MEGVYFNIDNGFIEGVVRGYRNGLLSNNQYINLTQCDTLEDLKLQLSSTDYGNFLSSVSS
ESLTTSLIQEYASSKLYHEFNYIRDQSSGSTRKFMDYITYGYMIDNVALMITGTIHDRDK
GEILQRCHPLGWFDTLPTLSVATDLESLYETVLVDTPLAPYFKNCFDTAEELDDMNIEII
RNKLYKAYLEDFYNFVTEEIPEPAKECMQTLLGFEADRRSINIALNSLQSSDIDPDLKSD
LLPNIGKLYPLATFHLAQAQDFEGVRAALANVYEYRGFLETGNLEDHFYQLEMELCRDAF
TQQFAISTVWAWMKSKEQEVRNITWIAECIAQNQRERINNYISVY

Sequence of entity 5 (C), FASTA

>6M0S_5 V-type proton ATPase subunit c'' (chains C)
SFSHFLYYLVLIVVIVYGLYKLFTGHGSDINFGKFLLRTSPYMWANLGIALCVGLSVVGA
AWGIFITGSSMIGAGVRAPRITTKNLISIIFCEVVAIYGLIIAIVFSSKLTVATAENMYS
KSNLYTGYSLFWAGITVGASNLICGIAVGITGATAAISDAADSALFVKILVIEIFGSILG
LLGLIVGLLMAGKASEFQ

Sequence of entity 6 (D), FASTA

>6M0S_6 V-type proton ATPase subunit c' (chains D)
SNIYAPLYAPFFGFAGCAAAMVLSCLGAAIGTAKSGIGIAGIGTFKPELIMKSLIPVVMS
GILAIYGLVVAVLIAGNLSPTEDYTLFNGFMHLSCGLCVGFACLSSGYAIGMVGDVGVRK
YMHQPRLFVGIVLILIFSEVLGLYGMIVALILNTRGSE

Sequence of entity 7 (E, F, G, H, I, J, K, L), FASTA

>6M0S_7 V-type proton ATPase subunit c (chains E, F, G, H, I, J, K, L)
MTELCPVYAPFFGAIGCASAIIFTSLGAAYGTAKSGVGICATCVLRPDLLFKNIVPVIMA
GIIAIYGLVVSVLVCYSLGQKQALYTGFIQLGAGLSVGLSGLAAGFAIGIVGDAGVRGSS
QQPRLFVGMILILIFAEVLGLYGLIVALLLNSRATQDVV

Sequence of entity 8 (N), FASTA

>6M0S_8 V0 assembly protein 1 (chains N)
DDILSSIWTEGLLMCLIVSALLLFILIVALSWISNLDITYGALEKSTNPIKK

Primary citation

Cryo-EM and MD infer water-mediated proton transport and autoinhibition mechanisms of V o complex. Roh, S.H., Shekhar, M., Pintilie, G. et al. Sci Adv (2020) 6. DOI 10.1126/sciadv.abb9605 · 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
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
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

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