8EAU: Yeast VO
Yeast VO in complex with Vma21p. Determined by electron microscopy at 3.1 Å resolution. Released 2 Nov 2022.
- Method
- Electron microscopy
- Resolution
- 3.1 Å
- Organism
- Saccharomyces cerevisiae
- Chains
- 16
- Atoms
- 21,909
- Mol. weight
- 361.86 kDa
- Released
- 2 Nov 2022
Explore 8EAU in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
8EAU contains 138 α-helices and 25 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: 45 helices, 22 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 4-6 | 3 | |
| β-strand | 10 | 1 | 1 |
| α-helix | 11-13 | 3 | |
| β-strand | 14-22 | 9 | 2 |
| α-helix | 23-25 | 3 | |
| α-helix | 26-36 | 11 | |
| β-strand | 39 | 1 | 3 |
| β-strand | 40-41 | 2 | 2 |
| α-helix | 50-52 | 3 | |
| α-helix | 56-78 | 23 | |
| α-helix | 88-92 | 5 | |
| α-helix | 101-103 | 3 | |
| α-helix | 106-145 | 40 | |
| β-strand | 185-192 | 8 | 4 |
| α-helix | 195-206 | 12 | |
| β-strand | 213-217 | 5 | 4 |
| β-strand | 222-224 | 3 | 5 |
| β-strand | 229-231 | 3 | 5 |
| β-strand | 233-240 | 8 | 4 |
| α-helix | 243-254 | 12 | |
| β-strand | 259-261 | 3 | 4 |
| α-helix | 267-323 | 57 | |
| β-strand | 327-329 | 3 | 2 |
| β-strand | 334-342 | 9 | 2 |
| α-helix | 343-345 | 3 | |
| α-helix | 346-360 | 15 | |
| β-strand | 367-371 | 5 | 2 |
| α-helix | 376-378 | 3 | |
| β-strand | 379 | 1 | 6 |
| α-helix | 388-394 | 7 | |
| α-helix | 399-401 | 3 | |
| β-strand | 405 | 1 | 1 |
| α-helix | 406 | 1 | |
| α-helix | 408-423 | 16 | |
| α-helix | 426-440 | 15 | |
| α-helix | 443-446 | 4 | |
| α-helix | 454-460 | 7 | |
| α-helix | 462-478 | 17 | |
| β-strand | 482 | 1 | 7 |
| β-strand | 485 | 1 | 7 |
| α-helix | 486-487 | 2 | |
| β-strand | 494-495 | 2 | 8 |
| β-strand | 506-507 | 2 | 9 |
| β-strand | 509-510 | 2 | 8 |
| α-helix | 520-522 | 3 | |
| α-helix | 528-561 | 34 | |
| α-helix | 565-567 | 3 | |
| α-helix | 568-572 | 5 | |
| α-helix | 573-579 | 7 | |
| α-helix | 580-584 | 5 | |
| α-helix | 585-595 | 11 | |
| α-helix | 598-601 | 4 | |
| α-helix | 603-606 | 4 | |
| α-helix | 608-617 | 10 | |
| α-helix | 630-659 | 30 | |
| α-helix | 712-732 | 21 | |
| α-helix | 735-750 | 16 | |
| α-helix | 751-755 | 5 | |
| α-helix | 758-760 | 3 | |
| α-helix | 764-780 | 17 | |
| α-helix | 781-788 | 8 | |
| α-helix | 790-799 | 10 | |
| α-helix | 800-805 | 6 | |
| α-helix | 806-809 | 4 | |
| β-strand | 816 | 1 | 6 |
| β-strand | 820 | 1 | 3 |
| α-helix | 827-830 | 4 | |
Chain b: 2 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 221-245 | 25 | |
| α-helix | 251-253 | 3 | |
Chain c: 10 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 17-38 | 22 | |
| α-helix | 42-44 | 3 | |
| α-helix | 47-53 | 7 | |
| α-helix | 56-89 | 34 | |
| α-helix | 96-122 | 27 | |
| α-helix | 130-132 | 3 | |
| α-helix | 136-176 | 41 | |
| α-helix | 178-180 | 3 | |
| α-helix | 181-207 | 27 | |
| α-helix | 209-212 | 4 | |
Chain d: 20 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 2-6 | 5 | |
| α-helix | 10-22 | 13 | |
| α-helix | 25-26 | 2 | |
| α-helix | 27-34 | 8 | |
| α-helix | 39-47 | 9 | |
| α-helix | 65-85 | 21 | |
| α-helix | 89-110 | 22 | |
| α-helix | 129-131 | 3 | |
| α-helix | 137-141 | 5 | |
| α-helix | 145-147 | 3 | |
| α-helix | 148-152 | 5 | |
| α-helix | 153-155 | 3 | |
| α-helix | 177-199 | 23 | |
| α-helix | 202-227 | 26 | |
| α-helix | 237-240 | 4 | |
| α-helix | 251-258 | 8 | |
| α-helix | 262-269 | 8 | |
| α-helix | 284-300 | 17 | |
| α-helix | 307-331 | 25 | |
| α-helix | 335-337 | 3 | |
Chain e: 3 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 5-24 | 20 | |
| α-helix | 30-54 | 25 | |
| β-strand | 63-64 | 2 | 9 |
| β-strand | 67 | 1 | 10 |
| α-helix | 69-71 | 3 | |
Chain f: 3 helices, 1 β-strand
| Element | Residues | Length | Sheet |
|---|
| α-helix | 7-32 | 26 | |
| α-helix | 36-39 | 4 | |
| β-strand | 41 | 1 | 10 |
| α-helix | 48-71 | 24 | |
Chain g: 6 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 9-43 | 35 | |
| α-helix | 47-49 | 3 | |
| α-helix | 50-53 | 4 | |
| α-helix | 55-75 | 21 | |
| α-helix | 84-121 | 38 | |
| α-helix | 125-151 | 27 | |
Chain h: 6 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 9-43 | 35 | |
| α-helix | 47-49 | 3 | |
| α-helix | 50-53 | 4 | |
| α-helix | 55-76 | 22 | |
| α-helix | 84-119 | 36 | |
| α-helix | 125-153 | 29 | |
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 | 840 | 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) |
| V-type proton ATPase subunit e | e | protein | 73 | Saccharomyces cerevisiae | Q3E7B6 |
| Yeast V-ATPase subunit f | 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 |
| Vacuolar ATPase assembly integral membrane protein VMA21 | p | protein | 77 | Saccharomyces cerevisiae | P41806 |
Sequence of entity 1 (a), FASTA
>8EAU_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
Sequence of entity 2 (b), FASTA
>8EAU_2 V0 assembly protein 1 (chains b)
MVFGQLYALFIFTLSCCISKTVQADSSKESSSFISFDKESNWDTISTISSTADVISSVDS
AIAVFEFDNFSLLDNLMIDEEYPFFNRFFANDVSLTVHDDSPLNISQSLSPIMEQFTVDE
LPESASDLLYEYSLDDKSIVLFKFTSDAYDLKKLDEFIDSCLSFLEDKSGDNLTVVINSL
GWAFEDEDGDDEYATEETLSHHDNNKGKEGDDDILSSIWTEGLLMCLIVSALLLFILIVA
LSWISNLDITYGALEKSTNPIKKNN
Sequence of entity 3 (c), FASTA
>8EAU_3 V-type proton ATPase subunit c'' (chains c)
MNKESKDDDMSLGKFSFSHFLYYLVLIVVIVYGLYKLFTGHGSDINFGKFLLRTSPYMWA
NLGIALCVGLSVVGAAWGIFITGSSMIGAGVRAPRITTKNLISIIFCEVVAIYGLIIAIV
FSSKLTVATAENMYSKSNLYTGYSLFWAGITVGASNLICGIAVGITGATAAISDAADSAL
FVKILVIEIFGSILGLLGLIVGLLMAGKASEFQ
Sequence of entity 4 (d), FASTA
>8EAU_4 V-type proton ATPase subunit d (chains d)
MEGVYFNIDNGFIEGVVRGYRNGLLSNNQYINLTQCDTLEDLKLQLSSTDYGNFLSSVSS
ESLTTSLIQEYASSKLYHEFNYIRDQSSGSTRKFMDYITYGYMIDNVALMITGTIHDRDK
GEILQRCHPLGWFDTLPTLSVATDLESLYETVLVDTPLAPYFKNCFDTAEELDDMNIEII
RNKLYKAYLEDFYNFVTEEIPEPAKECMQTLLGFEADRRSINIALNSLQSSDIDPDLKSD
LLPNIGKLYPLATFHLAQAQDFEGVRAALANVYEYRGFLETGNLEDHFYQLEMELCRDAF
TQQFAISTVWAWMKSKEQEVRNITWIAECIAQNQRERINNYISVY
Sequence of entity 5 (e), FASTA
>8EAU_5 V-type proton ATPase subunit e (chains e)
MSSFYTVVGVFIVVSAMSVLFWIMAPKNNQAVWRSTVILTLAMMFLMWAITFLCQLHPLV
APRRSDLRPEFAE
Sequence of entity 6 (f), FASTA
>8EAU_6 Yeast V-ATPase subunit f (chains f)
MRPVVSTGKAWCCTVLSAFGVVILSVIAHLFNTNHESFVGSINDPEDGPAVAHTVYLAAL
VYLVFFVFCGFQVYLARRKPSIELR
Sequence of entity 7 (g, h, i, j, k, l, m, n), FASTA
>8EAU_7 V-type proton ATPase subunit c (chains g, h, i, j, k, l, m, n)
MTELCPVYAPFFGAIGCASAIIFTSLGAAYGTAKSGVGICATCVLRPDLLFKNIVPVIMA
GIIAIYGLVVSVLVCYSLGQKQALYTGFIQLGAGLSVGLSGLAAGFAIGIVGDAGVRGSS
QQPRLFVGMILILIFAEVLGLYGLIVALLLNSRATQDVVC
Sequence of entity 8 (o), FASTA
>8EAU_8 V-type proton ATPase subunit c' (chains o)
MSTQLASNIYAPLYAPFFGFAGCAAAMVLSCLGAAIGTAKSGIGIAGIGTFKPELIMKSL
IPVVMSGILAIYGLVVAVLIAGNLSPTEDYTLFNGFMHLSCGLCVGFACLSSGYAIGMVG
DVGVRKYMHQPRLFVGIVLILIFSEVLGLYGMIVALILNTRGSE
Sequence of entity 9 (p), FASTA
>8EAU_9 Vacuolar ATPase assembly integral membrane protein VMA21 (chains p)
MAVDVPRAVINKLMLFTAAMVVLPVLTFFIIQQFTPNTLISGGLAAAMANVVLIVYIVVA
FREDTEDHKVDGNKKED
Primary citation
Structural basis of V-ATPase V O region assembly by Vma12p, 21p, and 22p. Wang, H., Bueler, S.A., Rubinstein, J.L. Proc Natl Acad Sci U S A (2023) 120:e2217181120-e2217181120. DOI 10.1073/pnas.2217181120 · 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
- 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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