6PE4: Yeast Vo motor
Yeast Vo motor in complex with 1 VopQ molecule. Determined by electron microscopy at 3.1 Å resolution. Released 20 May 2020.
- Method
- Electron microscopy
- Resolution
- 3.1 Å
- Organisms
- Saccharomyces cerevisiae (strain ATCC 204508 / S288c), Vibrio parahaemolyticus
- Chains
- 16
- Atoms
- 24,914
- Mol. weight
- 428.34 kDa
- Released
- 20 May 2020
Explore 6PE4 in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
6PE4 contains 152 α-helices and 19 β-strands across 16 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: 46 helices, 11 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 11-13 | 3 | |
| β-strand | 14-22 | 9 | 1 |
| α-helix | 23-25 | 3 | |
| α-helix | 26-35 | 10 | |
| β-strand | 40-41 | 2 | 1 |
| α-helix | 57-75 | 19 | |
| α-helix | 100-102 | 3 | |
| α-helix | 105-132 | 28 | |
| α-helix | 136-145 | 10 | |
| α-helix | 150-152 | 3 | |
| β-strand | 186-192 | 7 | 2 |
| α-helix | 193-195 | 3 | |
| α-helix | 196-206 | 11 | |
| β-strand | 214-217 | 4 | 2 |
| β-strand | 233-239 | 7 | 2 |
| α-helix | 244-255 | 12 | |
| β-strand | 259-261 | 3 | 2 |
| α-helix | 267-277 | 11 | |
| α-helix | 280-288 | 9 | |
| α-helix | 294-303 | 10 | |
| α-helix | 306-320 | 15 | |
| α-helix | 323-325 | 3 | |
| β-strand | 327-328 | 2 | 1 |
| β-strand | 334-342 | 9 | 1 |
| α-helix | 343-345 | 3 | |
| α-helix | 346-359 | 14 | |
| β-strand | 369-371 | 3 | 1 |
| α-helix | 388-395 | 8 | |
| α-helix | 399-401 | 3 | |
| α-helix | 404-406 | 3 | |
| α-helix | 411-422 | 12 | |
| α-helix | 426-440 | 15 | |
| α-helix | 455-460 | 6 | |
| α-helix | 462-478 | 17 | |
| β-strand | 482 | 1 | 3 |
| β-strand | 485 | 1 | 3 |
| α-helix | 520-522 | 3 | |
| α-helix | 528-551 | 24 | |
| α-helix | 553-559 | 7 | |
| α-helix | 565-567 | 3 | |
| α-helix | 568-572 | 5 | |
| α-helix | 573-579 | 7 | |
| α-helix | 585-594 | 10 | |
| α-helix | 604-607 | 4 | |
| α-helix | 608-614 | 7 | |
| α-helix | 630-647 | 18 | |
| α-helix | 651-657 | 7 | |
| α-helix | 712-722 | 11 | |
| α-helix | 726-731 | 6 | |
| α-helix | 732-734 | 3 | |
| α-helix | 735-750 | 16 | |
| α-helix | 751-755 | 5 | |
| α-helix | 757-760 | 4 | |
| α-helix | 765-782 | 18 | |
| α-helix | 783-787 | 5 | |
| α-helix | 788-802 | 15 | |
| α-helix | 828-831 | 4 | |
Chain B: 2 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 223-245 | 23 | |
| α-helix | 251-253 | 3 | |
Chain D: 18 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 3-6 | 4 | |
| α-helix | 11-21 | 11 | |
| α-helix | 27-34 | 8 | |
| α-helix | 39-46 | 8 | |
| α-helix | 65-84 | 20 | |
| α-helix | 90-115 | 26 | |
| α-helix | 120-124 | 5 | |
| α-helix | 136-140 | 5 | |
| β-strand | 144 | 1 | 4 |
| α-helix | 146-148 | 3 | |
| α-helix | 149-153 | 5 | |
| α-helix | 159-161 | 3 | |
| β-strand | 171 | 1 | 4 |
| α-helix | 174-199 | 26 | |
| α-helix | 202-225 | 24 | |
| α-helix | 235-238 | 4 | |
| α-helix | 252-256 | 5 | |
| α-helix | 262-269 | 8 | |
| α-helix | 285-298 | 14 | |
| α-helix | 307-330 | 24 | |
Chain E: 2 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 5-22 | 18 | |
| α-helix | 30-52 | 23 | |
Chain F: 2 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 11-32 | 22 | |
| α-helix | 53-70 | 18 | |
Chain G: 10 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 17-39 | 23 | |
| α-helix | 42-44 | 3 | |
| α-helix | 47-53 | 7 | |
| α-helix | 56-88 | 33 | |
| α-helix | 96-99 | 4 | |
| α-helix | 102-121 | 20 | |
| α-helix | 122-124 | 3 | |
| α-helix | 126-129 | 4 | |
| α-helix | 136-176 | 41 | |
| α-helix | 181-205 | 25 | |
Chain H: 7 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 15-47 | 33 | |
| α-helix | 53-55 | 3 | |
| α-helix | 61-80 | 20 | |
| α-helix | 92-125 | 34 | |
| α-helix | 131-133 | 3 | |
| α-helix | 134-143 | 10 | |
| α-helix | 146-162 | 17 | |
Chain I: 6 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 10-42 | 33 | |
| α-helix | 47-49 | 3 | |
| α-helix | 55-75 | 21 | |
| α-helix | 84-119 | 36 | |
| α-helix | 126-135 | 10 | |
| α-helix | 138-151 | 14 | |
8 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 | 1012 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | P32563 (AlphaFold model) |
| V0 assembly protein 1 | B | protein | 265 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | P53262 (AlphaFold model) |
| V-type proton ATPase subunit d | D | protein | 345 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | P32366 (AlphaFold model) |
| V-type proton ATPase subunit e | E | protein | 73 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | Q3E7B6 (AlphaFold model) |
| Uncharacterized protein YPR170W-B | F | protein | 85 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | P0C5R9 |
| V-type proton ATPase subunit c'' | G | protein | 213 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | P23968 |
| V-type proton ATPase subunit c' | H | protein | 164 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | P32842 |
| V-type proton ATPase subunit c | I, J, K, L, M, N, O, P | protein | 160 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | P25515 |
| Cation transporter | Q | protein | 513 | Vibrio parahaemolyticus | Q87P38 |
Sequence of entity 1 (A), FASTA
>6PE4_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
SMEKRRWKKNFIAVSAANRFKKISSSGALDYDIPTTASENLYFQGELKTAALAQHDEAVD
NFNKEQQNAFYEILHLPNLNEEQRNAFIQSLKDDPSQSANLLAEAKKLNDAQAPKVDNFN
KEQQNAFYEILHLPNLNEEQRNAFIQSLKDDPSQSANLLAEAKKLNDAQAPK
Sequence of entity 2 (B), FASTA
>6PE4_2 V0 assembly protein 1 (chains B)
MVFGQLYALFIFTLSCCISKTVQADSSKESSSFISFDKESNWDTISTISSTADVISSVDS
AIAVFEFDNFSLLDNLMIDEEYPFFNRFFANDVSLTVHDDSPLNISQSLSPIMEQFTVDE
LPESASDLLYEYSLDDKSIVLFKFTSDAYDLKKLDEFIDSCLSFLEDKSGDNLTVVINSL
GWAFEDEDGDDEYATEETLSHHDNNKGKEGDDDILSSIWTEGLLMCLIVSALLLFILIVA
LSWISNLDITYGALEKSTNPIKKNN
Sequence of entity 3 (D), FASTA
>6PE4_3 V-type proton ATPase subunit d (chains D)
MEGVYFNIDNGFIEGVVRGYRNGLLSNNQYINLTQCDTLEDLKLQLSSTDYGNFLSSVSS
ESLTTSLIQEYASSKLYHEFNYIRDQSSGSTRKFMDYITYGYMIDNVALMITGTIHDRDK
GEILQRCHPLGWFDTLPTLSVATDLESLYETVLVDTPLAPYFKNCFDTAEELDDMNIEII
RNKLYKAYLEDFYNFVTEEIPEPAKECMQTLLGFEADRRSINIALNSLQSSDIDPDLKSD
LLPNIGKLYPLATFHLAQAQDFEGVRAALANVYEYRGFLETGNLEDHFYQLEMELCRDAF
TQQFAISTVWAWMKSKEQEVRNITWIAECIAQNQRERINNYISVY
Sequence of entity 4 (E), FASTA
>6PE4_4 V-type proton ATPase subunit e (chains E)
MSSFYTVVGVFIVVSAMSVLFWIMAPKNNQAVWRSTVILTLAMMFLMWAITFLCQLHPLV
APRRSDLRPEFAE
Sequence of entity 5 (F), FASTA
>6PE4_5 Uncharacterized protein YPR170W-B (chains F)
MRPVVSTGKAWCCTVLSAFGVVILSVIAHLFNTNHESFVGSINDPEDGPAVAHTVYLAAL
VYLVFFVFCGFQVYLARRKPSIELR
Sequence of entity 6 (G), FASTA
>6PE4_6 V-type proton ATPase subunit c'' (chains G)
MNKESKDDDMSLGKFSFSHFLYYLVLIVVIVYGLYKLFTGHGSDINFGKFLLRTSPYMWA
NLGIALCVGLSVVGAAWGIFITGSSMIGAGVRAPRITTKNLISIIFCEVVAIYGLIIAIV
FSSKLTVATAENMYSKSNLYTGYSLFWAGITVGASNLICGIAVGITGATAAISDAADSAL
FVKILVIEIFGSILGLLGLIVGLLMAGKASEFQ
Sequence of entity 7 (H), FASTA
>6PE4_7 V-type proton ATPase subunit c' (chains H)
MSTQLASNIYAPLYAPFFGFAGCAAAMVLSCLGAAIGTAKSGIGIAGIGTFKPELIMKSL
IPVVMSGILAIYGLVVAVLIAGNLSPTEDYTLFNGFMHLSCGLCVGFACLSSGYAIGMVG
DVGVRKYMHQPRLFVGIVLILIFSEVLGLYGMIVALILNTRGSE
Sequence of entity 8 (I, J, K, L, M, N, O, P), FASTA
>6PE4_8 V-type proton ATPase subunit c (chains I, J, K, L, M, N, O, P)
MTELCPVYAPFFGAIGCASAIIFTSLGAAYGTAKSGVGICATCVLRPDLLFKNIVPVIMA
GIIAIYGLVVSVLVCYSLGQKQALYTGFIQLGAGLSVGLSGLAAGFAIGIVGDAGVRGSS
QQPRLFVGMILILIFAEVLGLYGLIVALLLNSRATQDVVC
Sequence of entity 9 (Q), FASTA
>6PE4_9 Cation transporter (chains Q)
MGSSHHHHHHSQDLDEVDAGSMVNTTQKISQSPVPDLEQFRAIAAQKDDRVISKRGEVKE
PSTFHKGHKFASVSEGVLRKKYTKFFQENIKTHLDLKQALLKEEKPETALLAYSLVSPSG
YRGEPLTERKILEVVSLLDEVKVDGDTYQQLKNTFDSISKDPRMQVSLENQYPGKMDGFG
AQLLEMGKEKLKGSGVNAAINLALPGVGLLVATGRELHKASVNGDAEAYHHQLEQISQLP
GRDQRLSMPMQQTLAIGHAMLSAEGAVGATLGMATGGLGTFGVSSVATAGVTPIAKEAIG
TALTTGIISGGGFVAGQAGAYGLNNEVQDQLKQGPMSGVLPRLEISNVKGDFTFSMQEPA
AVRALMAYLGPKEDTSMSSPQAPKEAQEMEAARLTLKQMLGSSPNEHLVPDVDSLLKLSD
EDMPSQTESTANGAFKKLLSEDWDWLMPAVRAMDKGEAGKINEKLTYKLPLDAANGRVYL
DKSPNLSDAQLDALDKLGSPSQLRLMYLAEGWI
Primary citation
A distinct inhibitory mechanism of the V-ATPase by Vibrio VopQ revealed by cryo-EM. Peng, W., Casey, A.K., Fernandez, J. et al. Nat Struct Mol Biol (2020) 27:589-597. DOI 10.1038/s41594-020-0429-1 · 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
- 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
- 6M0S 3.6 Å, 3.6A Yeast Vo state3 prime
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