6M0R: 2.7A Yeast Vo state3

2.7A Yeast Vo state3. Determined by electron microscopy at 2.7 Å resolution. Released 4 Nov 2020.

Method
Electron microscopy
Resolution
2.7 Å
Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Chains
15
Atoms
23,667
Mol. weight
346.83 kDa
Ligands
PEE, PPV, EYR
Released
4 Nov 2020

Explore 6M0R in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6M0R contains 138 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: 40 helices, 18 β-strands

ElementResiduesLengthSheet
β-strand1013
α-helix11-133
β-strand14-2184
α-helix26-3611
β-strand40-4124
α-helix56-7823
α-helix81-844
α-helix104-14643
α-helix150-1523
β-strand186-19275
α-helix193-1953
α-helix196-20611
β-strand213-21755
β-strand222-22326
β-strand230-23126
β-strand233-23975
α-helix243-25513
β-strand259-26025
α-helix267-30236
α-helix309-32416
β-strand327-32824
β-strand335-34284
α-helix343-3453
α-helix347-36014
β-strand368-37144
α-helix377-3793
α-helix388-39710
α-helix399-4013
β-strand40513
α-helix411-42313
α-helix426-44116
α-helix443-4486
α-helix454-4607
α-helix464-47916
β-strand48217
β-strand48517
α-helix491-4922
β-strand494-49528
β-strand506-50721
β-strand509-51028
α-helix520-5223
α-helix528-56235
α-helix565-5673
α-helix568-5725
α-helix573-5797
α-helix580-5845
α-helix585-59410
α-helix598-6014
α-helix603-6075
α-helix608-61710
α-helix630-65829
α-helix707-73226
α-helix735-75824
α-helix764-78219
α-helix783-7886
α-helix789-79911
α-helix800-8056
α-helix806-8083
Chain B: 22 helices, 0 β-strands
ElementResiduesLengthSheet
α-helix2-54
α-helix7-2216
α-helix25-262
α-helix27-348
α-helix39-468
α-helix65-8622
α-helix90-978
α-helix100-11516
α-helix120-1245
α-helix129-1313
α-helix137-1404
α-helix145-1484
α-helix149-1535
α-helix159-1657
α-helix174-19825
α-helix204-22926
α-helix235-2384
α-helix251-2577
α-helix262-2698
α-helix284-29916
α-helix308-33124
α-helix338-3403
Chain C: 8 helices, 0 β-strands
ElementResiduesLengthSheet
α-helix17-3822
α-helix42-443
α-helix47-537
α-helix56-8934
α-helix94-963
α-helix102-12221
α-helix136-17641
α-helix180-20526
Chain D: 6 helices, 0 β-strands
ElementResiduesLengthSheet
α-helix15-4834
α-helix53-553
α-helix61-8222
α-helix92-12736
α-helix131-1333
α-helix134-16330
Chain E: 6 helices, 0 β-strands
ElementResiduesLengthSheet
α-helix10-4536
α-helix47-493
α-helix55-7521
α-helix84-11936
α-helix123-1253
α-helix129-15325
Chain F: 8 helices, 0 β-strands
ElementResiduesLengthSheet
α-helix9-4537
α-helix47-504
α-helix52-543
α-helix55-7521
α-helix84-11936
α-helix123-1253
α-helix126-13712
α-helix139-15416
Chain G: 6 helices, 0 β-strands
ElementResiduesLengthSheet
α-helix11-4232
α-helix50-523
α-helix55-7723
α-helix84-12138
α-helix123-1253
α-helix126-15328
Chain H: 9 helices, 0 β-strands
ElementResiduesLengthSheet
α-helix11-144
α-helix16-4227
α-helix47-493
α-helix55-7521
α-helix84-11936
α-helix123-1253
α-helix126-13712
α-helix139-15012
α-helix151-1533

7 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
V-type proton ATPase subunit c'Dprotein158Saccharomyces cerevisiae (strain ATCC 204508 / S288c)P32842 (AlphaFold model)
V-type proton ATPase subunit c''Cprotein198Saccharomyces cerevisiae (strain ATCC 204508 / S288c)P23968 (AlphaFold model)
V0 assembly protein 1Nprotein52Saccharomyces cerevisiae (strain ATCC 204508 / S288c)P53262 (AlphaFold model)
V-type proton ATPase subunit eMprotein71Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Q3E7B6 (AlphaFold model)
V-type proton ATPase subunit cE, F, G, H, I, J, K, Lprotein159Saccharomyces cerevisiae (strain ATCC 204508 / S288c)P25515
Uncharacterized protein YPR170W-BOprotein69Saccharomyces cerevisiae (strain ATCC 204508 / S288c)P0C5R9
V-type proton ATPase subunit dBprotein345Saccharomyces cerevisiae (strain ATCC 204508 / S288c)P32366
V-type proton ATPase subunit a, vacuolar isoformAprotein825Saccharomyces cerevisiae (strain ATCC 204508 / S288c)P32563
Sequence of entity 1 (D), FASTA
>6M0R_1 V-type proton ATPase subunit c' (chains D)
SNIYAPLYAPFFGFAGCAAAMVLSCLGAAIGTAKSGIGIAGIGTFKPELIMKSLIPVVMS
GILAIYGLVVAVLIAGNLSPTEDYTLFNGFMHLSCGLCVGFACLSSGYAIGMVGDVGVRK
YMHQPRLFVGIVLILIFSEVLGLYGMIVALILNTRGSE
Sequence of entity 2 (C), FASTA
>6M0R_2 V-type proton ATPase subunit c'' (chains C)
SFSHFLYYLVLIVVIVYGLYKLFTGHGSDINFGKFLLRTSPYMWANLGIALCVGLSVVGA
AWGIFITGSSMIGAGVRAPRITTKNLISIIFCEVVAIYGLIIAIVFSSKLTVATAENMYS
KSNLYTGYSLFWAGITVGASNLICGIAVGITGATAAISDAADSALFVKILVIEIFGSILG
LLGLIVGLLMAGKASEFQ
Sequence of entity 3 (N), FASTA
>6M0R_3 V0 assembly protein 1 (chains N)
DDILSSIWTEGLLMCLIVSALLLFILIVALSWISNLDITYGALEKSTNPIKK
Sequence of entity 4 (M), FASTA
>6M0R_4 V-type proton ATPase subunit e (chains M)
MSSFYTVVGVFIVVSAMSVLFWIMAPKNNQAVWRSTVILTLAMMFLMWAITFLCQLHPLV
APRRSDLRPEF
Sequence of entity 5 (E, F, G, H, I, J, K, L), FASTA
>6M0R_5 V-type proton ATPase subunit c (chains E, F, G, H, I, J, K, L)
MTELCPVYAPFFGAIGCASAIIFTSLGAAYGTAKSGVGICATCVLRPDLLFKNIVPVIMA
GIIAIYGLVVSVLVCYSLGQKQALYTGFIQLGAGLSVGLSGLAAGFAIGIVGDAGVRGSS
QQPRLFVGMILILIFAEVLGLYGLIVALLLNSRATQDVV
Sequence of entity 6 (O), FASTA
>6M0R_6 Uncharacterized protein YPR170W-B (chains O)
TGKAWCCTVLSAFGVVILSVIAHLFNTNHESFVGSINDPEDGPAVAHTVYLAALVYLVFF
VFCGFQVYL
Sequence of entity 7 (B), FASTA
>6M0R_7 V-type proton ATPase subunit d (chains B)
MEGVYFNIDNGFIEGVVRGYRNGLLSNNQYINLTQCDTLEDLKLQLSSTDYGNFLSSVSS
ESLTTSLIQEYASSKLYHEFNYIRDQSSGSTRKFMDYITYGYMIDNVALMITGTIHDRDK
GEILQRCHPLGWFDTLPTLSVATDLESLYETVLVDTPLAPYFKNCFDTAEELDDMNIEII
RNKLYKAYLEDFYNFVTEEIPEPAKECMQTLLGFEADRRSINIALNSLQSSDIDPDLKSD
LLPNIGKLYPLATFHLAQAQDFEGVRAALANVYEYRGFLETGNLEDHFYQLEMELCRDAF
TQQFAISTVWAWMKSKEQEVRNITWIAECIAQNQRERINNYISVY
Sequence of entity 8 (A), FASTA
>6M0R_8 V-type proton ATPase subunit a, vacuolar isoform (chains A)
EKEEAIFRSAEMALVQFYIPQEISRDSAYTLGQLGLVQFRDLNSKVRAFQRTFVNEIRRL
DNVERQYRYFYSLLKKHDIKLYEGDTDKYLDGSGELYVPPSGSVIDDYVRNASYLEERLI
QMEDATDQIEVQKNDLEQYRFILQSGDEFFLKGDNTDSTSYMDEDMIDANGENIAAAIGA
SVNYVTGVIARDKVATLEQILWRVLRGNLFFKTVEIEQPVYDVKTREYKHKNAFIVFSHG
DLIIKRIRKIAESLDANLYDVDSSNEGRSQQLAKVNKNLSDLYTVLKTTSTTLESELYAI
AKELDSWFQDVTREKAIFEILNKSNYDTNRKILIAEGWIPRDELATLQARLGEMIARLGI
DVPSIIQVLDTNHTPPTFHRTNKFTAGFQSICDCYGIAQYREINAGLPTIVTFPFMFAIM
FGDMGHGFLMTLAALSLVLNEKKINKMKRGEIFDMAFTGRYIILLMGVFSMYTGFLYNDI
FSKTMTIFKSGWKWPDHWKKGESITATSVGTYPIGLDWAWHGTENALLFSNSYKMKLSIL
MGFIHMTYSYFFSLANHLYFNSMIDIIGNFIPGLLFMQGIFGYLSVCIVYKWAVDWVKDG
KPAPGLLNMLINMFLSPGTIDDELYPHQAKVQVFLLLMALVCIPWLLLVKPLHFKFTHKK
KSHEPLPSTEADASSEDLEAQQLISAMDADDAEEEEVGSGSHGEDFGDIMIHQVIHTIEF
CLNCVSHTASYLRLWALSLAHAQLSSVLWTMTIQIAFGFRGFVGVFMTVALFAMWFALTC
AVLVLMEGTSAMLHSLRLHWVESMSKFFVGEGLPYEPFAFEYKDM

Ligands and cofactors

IDNameFormulaCopies
PEE1,2-dioleoyl-sn-glycero-3-phosphoethanolamineC41 H78 N O8 P30
PPVPyrophosphateH4 O7 P21
EYR(6~{E},10~{E},14~{E},18~{E},22~{E},26~{E},30~{R})-2,6,10,14,18,22,26,30-octamet…C40 H681

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 P32842 (AlphaFold model), which also has an AlphaFold model), best resolution first:

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