5TJ5: V-type proton ATPase subunit a
Atomic model for the membrane-embedded motor of a eukaryotic V-ATPase. Determined by electron microscopy at 3.9 Å resolution. Released 26 Oct 2016.
- Method
- Electron microscopy
- Resolution
- 3.9 Å
- Organism
- Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
- Chains
- 14
- Atoms
- 14,976
- Mol. weight
- 273.56 kDa
- Released
- 26 Oct 2016
Explore 5TJ5 in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
5TJ5 contains 113 α-helices and 0 β-strands across 14 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: 24 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 7-33 | 27 | |
| α-helix | 59-95 | 37 | |
| α-helix | 124-175 | 52 | |
| α-helix | 199-206 | 8 | |
| α-helix | 279-294 | 16 | |
| α-helix | 311-315 | 5 | |
| α-helix | 354-363 | 10 | |
| α-helix | 411-420 | 10 | |
| α-helix | 430-441 | 12 | |
| α-helix | 443-449 | 7 | |
| α-helix | 453-460 | 8 | |
| α-helix | 462-479 | 18 | |
| α-helix | 532-557 | 26 | |
| α-helix | 578-593 | 16 | |
| α-helix | 608-613 | 6 | |
| α-helix | 632-656 | 25 | |
| α-helix | 711-732 | 22 | |
| α-helix | 735-752 | 18 | |
| α-helix | 755-758 | 4 | |
| α-helix | 764-791 | 28 | |
| α-helix | 793-796 | 4 | |
| α-helix | 797-803 | 7 | |
| α-helix | 804-807 | 4 | |
| α-helix | 817-828 | 12 | |
Chain B: 9 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 3-22 | 20 | |
| α-helix | 32-46 | 15 | |
| α-helix | 62-90 | 29 | |
| α-helix | 98-100 | 3 | |
| α-helix | 101-120 | 20 | |
| α-helix | 140-172 | 33 | |
| α-helix | 182-190 | 9 | |
| α-helix | 193-207 | 15 | |
| α-helix | 210-212 | 3 | |
Chain D: 5 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 20-45 | 26 | |
| α-helix | 61-83 | 23 | |
| α-helix | 96-129 | 34 | |
| α-helix | 131-133 | 3 | |
| α-helix | 134-161 | 28 | |
Chain E: 6 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 12-14 | 3 | |
| α-helix | 15-36 | 22 | |
| α-helix | 54-78 | 25 | |
| α-helix | 84-121 | 38 | |
| α-helix | 126-136 | 11 | |
| α-helix | 138-153 | 16 | |
Chains F, G, H, I, J, M and N: 7 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 12-14 | 3 | |
| α-helix | 15-43 | 29 | |
| α-helix | 50-53 | 4 | |
| α-helix | 55-76 | 22 | |
| α-helix | 86-121 | 36 | |
| α-helix | 126-136 | 11 | |
| α-helix | 138-152 | 15 | |
Chain L: 3 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 7-15 | 9 | |
| α-helix | 16-18 | 3 | |
| α-helix | 30-46 | 17 | |
Chain O: 2 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 3-24 | 22 | |
| α-helix | 79-99 | 21 | |
Chain P: 15 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 11-21 | 11 | |
| α-helix | 25-26 | 2 | |
| α-helix | 27-34 | 8 | |
| α-helix | 39-48 | 10 | |
| α-helix | 65-85 | 21 | |
| α-helix | 90-111 | 22 | |
| α-helix | 130-133 | 4 | |
| α-helix | 145-148 | 4 | |
| α-helix | 160-162 | 3 | |
| α-helix | 177-195 | 19 | |
| α-helix | 205-227 | 23 | |
| α-helix | 238-241 | 4 | |
| α-helix | 251-256 | 6 | |
| α-helix | 285-299 | 15 | |
| α-helix | 308-332 | 25 | |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| V-type proton ATPase subunit a | A | protein | 680 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | P32563 (AlphaFold model) |
| V-type proton ATPase subunit c'' | B | protein | 213 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | P23968 (AlphaFold model) |
| V-type proton ATPase subunit c' | D | protein | 147 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | P32842 (AlphaFold model) |
| V-type proton ATPase subunit c | E, F, G, H, I, J, M, N | protein | 150 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | P25515 (AlphaFold model) |
| V-type proton ATPase subunit e | L | protein | 57 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | Q3E7B6 |
| V-type proton ATPase subunit f | O | protein | 54 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | |
| V-type proton ATPase subunit d | P | protein | 297 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | P32366 |
Sequence of entity 1 (A), FASTA
>5TJ5_1 V-type proton ATPase subunit a (chains A)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Sequence of entity 2 (B), FASTA
>5TJ5_2 V-type proton ATPase subunit c'' (chains B)
MNKESKDDDMSLGKFSFSHFLYYLVLIVVIVYGLYKLFTGHGSDINFGKFLLRTSPYMWA
NLGIALCVGLSVVGAAWGIFITGSSMIGAGVRAPRITTKNLISIIFCEVVAIYGLIIAIV
FSSKLTVATAENMYSKSNLYTGYSLFWAGITVGASNLICGIAVGITGATAAISDAADSAL
FVKILVIEIFGSILGLLGLIVGLLMAGKASEFQ
Sequence of entity 3 (D), FASTA
>5TJ5_3 V-type proton ATPase subunit c' (chains D)
FFGFAGCAAAMVLSCLGAAIGTAKSGIGIAGIGTFKPELIMKSLIPVVMSGILAIYGLVV
AVLIAGNLSPTEDYTLFNGFMHLSCGLCVGFACLSSGYAIGMVGDVGVRKYMHQPRLFVG
IVLILIFSEVLGLYGMIVALILNTRGS
Sequence of entity 4 (E, F, G, H, I, J, M, N), FASTA
>5TJ5_4 V-type proton ATPase subunit c (chains E, F, G, H, I, J, M, N)
APFFGAIGCASAIIFTSLGAAYGTAKSGVGICATCVLRPDLLFKNIVPVIMAGIIAIYGL
VVSVLVCYSLGQKQALYTGFIQLGAGLSVGLSGLAAGFAIGIVGDAGVRGSSQQPRLFVG
MILILIFAEVLGLYGLIVALLLNSRATQDV
Sequence of entity 5 (L), FASTA
>5TJ5_5 V-type proton ATPase subunit e (chains L)
YTVVGVFIVVSAMSVLFWIMAPKNNQAVWRSTVILTLAMMFLMWAITFLCQLHPLVA
Sequence of entity 6 (O), FASTA
>5TJ5_6 V-type proton ATPase subunit f (chains O)
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
Sequence of entity 7 (P), FASTA
>5TJ5_7 V-type proton ATPase subunit d (chains P)
VYFNIDNGFIEGVVRGYRNGLLSNNQYINLTQCDTLEDLKLQLSSTDYGNFLSSVSSESL
TTSLIQEYASSKLYHEFNYIRDQSSGSTRKFMDYITYGYMIDNVALMITGTIHDRDKGEI
LQRCHPLGWFDTLPTLSVATDLESLYETVLVDXXXXXXXXXXXXXXXXXXXXNIEIIRNK
LYKAYLEDFYNFVTEEIPXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXL
EDHFYQLEMELCRDAFTQQFAISTVWAWMKSKEQEVRNITWIAECIAQNQRERINNY
Primary citation
Atomic model for the membrane-embedded VO motor of a eukaryotic V-ATPase. Mazhab-Jafari, M.T., Rohou, A., Schmidt, C. et al. Nature (2016) 539:118-122. DOI 10.1038/nature19828 · 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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