6C6L: Yeast Vacuolar ATPase Vo in lipid nanodisc

Yeast Vacuolar ATPase Vo in lipid nanodisc. Determined by electron microscopy at 3.5 Å resolution. Released 21 Mar 2018.

Method: Electron microscopy
Resolution: 3.5 Å
Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Chains: 15
Atoms: 22,110
Mol. weight: 353.42 kDa
Released: 21 Mar 2018

Explore 6C6L in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6C6L contains 113 α-helices and 15 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, 15 β-strands

Element	Residues	Length	Sheet
β-strand	10	1	1
α-helix	11-13	3
β-strand	14-22	9	2
α-helix	26-35	10
β-strand	40-42	3	2
α-helix	43	1
α-helix	56-78	23
α-helix	88-92	5
α-helix	100-103	4
α-helix	107-144	38
β-strand	186-192	7	3
α-helix	193-195	3
α-helix	196-207	12
β-strand	212-217	6	3
β-strand	233-239	7	3
α-helix	243-255	13
β-strand	258-261	4	3
α-helix	268-324	57
β-strand	327-329	3	2
β-strand	334-342	9	2
α-helix	343-358	16
β-strand	369-370	2	2
β-strand	378-379	2	4
α-helix	388-394	7
β-strand	405	1	1
α-helix	408-422	15
α-helix	426-441	16
α-helix	443-446	4
α-helix	450-451	2
α-helix	455-460	6
α-helix	462-479	18
β-strand	495	1	5
β-strand	509	1	5
α-helix	520-522	3
α-helix	527-553	27
α-helix	555-559	5
α-helix	569-595	27
α-helix	610-617	8
α-helix	630-651	22
α-helix	710-731	22
α-helix	734-750	17
α-helix	751-755	5
α-helix	756-758	3
α-helix	765-779	15
α-helix	780-784	5
α-helix	785-799	15
α-helix	800-806	7
α-helix	807-809	3
β-strand	815-816	2	4

Chain B: 17 helices, 0 β-strands

Element	Residues	Length
α-helix	5-8	4
α-helix	11-21	11
α-helix	27-34	8
α-helix	39-46	8
α-helix	65-85	21
α-helix	89-115	27
α-helix	120-126	7
α-helix	145-155	11
α-helix	174-198	25
α-helix	203-230	28
α-helix	235-241	7
α-helix	244-246	3
α-helix	252-257	6
α-helix	262-268	7
α-helix	284-299	16
α-helix	308-331	24
α-helix	336-340	5

Chain C: 9 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	102-122	21
α-helix	136-172	37
α-helix	181-184	4
α-helix	186-191	6
α-helix	193-207	15

Chain D: 6 helices, 0 β-strands

Element	Residues	Length
α-helix	15-48	34
α-helix	56-59	4
α-helix	61-80	20
α-helix	92-123	32
α-helix	126-128	3
α-helix	134-159	26

Chain E: 6 helices, 0 β-strands

Element	Residues	Length
α-helix	10-42	33
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: 4 helices, 0 β-strands

Element	Residues	Length
α-helix	9-42	34
α-helix	55-75	21
α-helix	85-121	37
α-helix	125-152	28

Chain G: 5 helices, 0 β-strands

Element	Residues	Length
α-helix	10-42	33
α-helix	48-50	3
α-helix	57-75	19
α-helix	84-121	38
α-helix	126-152	27

Chains H and K: 5 helices, 0 β-strands

Element	Residues	Length
α-helix	10-42	33
α-helix	47-49	3
α-helix	55-75	21
α-helix	84-121	38
α-helix	125-154	30

6 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 (strain ATCC 204508 / S288c)	P32842 (AlphaFold model)
V-type proton ATPase subunit c''	C	protein	213	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P23968 (AlphaFold model)
V0 assembly protein 1	N	protein	265	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P53262 (AlphaFold model)
V-type proton ATPase subunit e	M	protein	73	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Q3E7B6 (AlphaFold model)
V-type proton ATPase subunit c	E, F, G, H, I, J, K, L	protein	160	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P25515
V-type proton ATPase subunit d	B	protein	345	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P32366
V-type proton ATPase subunit a, vacuolar isoform	A	protein	840	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P32563
V-type proton ATPase subunit f	O	protein	85	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P0C5R9

Sequence of entity 1 (D), FASTA

>6C6L_1 V-type proton ATPase subunit c' (chains D)
MSTQLASNIYAPLYAPFFGFAGCAAAMVLSCLGAAIGTAKSGIGIAGIGTFKPELIMKSL
IPVVMSGILAIYGLVVAVLIAGNLSPTEDYTLFNGFMHLSCGLCVGFACLSSGYAIGMVG
DVGVRKYMHQPRLFVGIVLILIFSEVLGLYGMIVALILNTRGSE

Sequence of entity 2 (C), FASTA

>6C6L_2 V-type proton ATPase subunit c'' (chains C)
MNKESKDDDMSLGKFSFSHFLYYLVLIVVIVYGLYKLFTGHGSDINFGKFLLRTSPYMWA
NLGIALCVGLSVVGAAWGIFITGSSMIGAGVRAPRITTKNLISIIFCEVVAIYGLIIAIV
FSSKLTVATAENMYSKSNLYTGYSLFWAGITVGASNLICGIAVGITGATAAISDAADSAL
FVKILVIEIFGSILGLLGLIVGLLMAGKASEFQ

Sequence of entity 3 (N), FASTA

>6C6L_3 V0 assembly protein 1 (chains N)
MVFGQLYALFIFTLSCCISKTVQADSSKESSSFISFDKESNWDTISTISSTADVISSVDS
AIAVFEFDNFSLLDNLMIDEEYPFFNRFFANDVSLTVHDDSPLNISQSLSPIMEQFTVDE
LPESASDLLYEYSLDDKSIVLFKFTSDAYDLKKLDEFIDSCLSFLEDKSGDNLTVVINSL
GWAFEDEDGDDEYATEETLSHHDNNKGKEGDDDILSSIWTEGLLMCLIVSALLLFILIVA
LSWISNLDITYGALEKSTNPIKKNN

Sequence of entity 4 (M), FASTA

>6C6L_4 V-type proton ATPase subunit e (chains M)
MSSFYTVVGVFIVVSAMSVLFWIMAPKNNQAVWRSTVILTLAMMFLMWAITFLCQLHPLV
APRRSDLRPEFAE

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

>6C6L_5 V-type proton ATPase subunit c (chains E, F, G, H, I, J, K, L)
MTELCPVYAPFFGAIGCASAIIFTSLGAAYGTAKSGVGICATCVLRPDLLFKNIVPVIMA
GIIAIYGLVVSVLVCYSLGQKQALYTGFIQLGAGLSVGLSGLAAGFAIGIVGDAGVRGSS
QQPRLFVGMILILIFAEVLGLYGLIVALLLNSRATQDVVC

Sequence of entity 6 (B), FASTA

>6C6L_6 V-type proton ATPase subunit d (chains B)
MEGVYFNIDNGFIEGVVRGYRNGLLSNNQYINLTQCDTLEDLKLQLSSTDYGNFLSSVSS
ESLTTSLIQEYASSKLYHEFNYIRDQSSGSTRKFMDYITYGYMIDNVALMITGTIHDRDK
GEILQRCHPLGWFDTLPTLSVATDLESLYETVLVDTPLAPYFKNCFDTAEELDDMNIEII
RNKLYKAYLEDFYNFVTEEIPEPAKECMQTLLGFEADRRSINIALNSLQSSDIDPDLKSD
LLPNIGKLYPLATFHLAQAQDFEGVRAALANVYEYRGFLETGNLEDHFYQLEMELCRDAF
TQQFAISTVWAWMKSKEQEVRNITWIAECIAQNQRERINNYISVY

Sequence of entity 7 (A), FASTA

>6C6L_7 V-type proton ATPase subunit a, vacuolar isoform (chains A)
MAEKEEAIFRSAEMALVQFYIPQEISRDSAYTLGQLGLVQFRDLNSKVRAFQRTFVNEIR
RLDNVERQYRYFYSLLKKHDIKLYEGDTDKYLDGSGELYVPPSGSVIDDYVRNASYLEER
LIQMEDATDQIEVQKNDLEQYRFILQSGDEFFLKGDNTDSTSYMDEDMIDANGENIAAAI
GASVNYVTGVIARDKVATLEQILWRVLRGNLFFKTVEIEQPVYDVKTREYKHKNAFIVFS
HGDLIIKRIRKIAESLDANLYDVDSSNEGRSQQLAKVNKNLSDLYTVLKTTSTTLESELY
AIAKELDSWFQDVTREKAIFEILNKSNYDTNRKILIAEGWIPRDELATLQARLGEMIARL
GIDVPSIIQVLDTNHTPPTFHRTNKFTAGFQSICDCYGIAQYREINAGLPTIVTFPFMFA
IMFGDMGHGFLMTLAALSLVLNEKKINKMKRGEIFDMAFTGRYIILLMGVFSMYTGFLYN
DIFSKTMTIFKSGWKWPDHWKKGESITATSVGTYPIGLDWAWHGTENALLFSNSYKMKLS
ILMGFIHMTYSYFFSLANHLYFNSMIDIIGNFIPGLLFMQGIFGYLSVCIVYKWAVDWVK
DGKPAPGLLNMLINMFLSPGTIDDELYPHQAKVQVFLLLMALVCIPWLLLVKPLHFKFTH
KKKSHEPLPSTEADASSEDLEAQQLISAMDADDAEEEEVGSGSHGEDFGDIMIHQVIHTI
EFCLNCVSHTASYLRLWALSLAHAQLSSVLWTMTIQIAFGFRGFVGVFMTVALFAMWFAL
TCAVLVLMEGTSAMLHSLRLHWVESMSKFFVGEGLPYEPFAFEYKDMEVAVASASSSASS

Sequence of entity 8 (O), FASTA

>6C6L_8 V-type proton ATPase subunit f (chains O)
MRPVVSTGKAWCCTVLSAFGVVILSVIAHLFNTNHESFVGSINDPEDGPAVAHTVYLAAL
VYLVFFVFCGFQVYLARRKPSIELR

Primary citation

The 3.5- angstrom CryoEM Structure of Nanodisc-Reconstituted Yeast Vacuolar ATPase VoProton Channel. Roh, S.H., Stam, N.J., Hryc, C.F. et al. Mol Cell (2018) 69:993-1004.e3. DOI 10.1016/j.molcel.2018.02.006 · 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
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

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