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- PDB-36qx: Arabidopsis thaliana V-type ATPase, State 1 bound to OXR5, Backbo... -

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Basic information

Entry
Database: PDB / ID: 36qx
TitleArabidopsis thaliana V-type ATPase, State 1 bound to OXR5, Backbone model
Components
  • (V-type proton ATPase subunit ...) x 14
  • TLD-domain containing nucleolar protein OXR5
  • V-type proton ATPase catalytic subunit A
KeywordsHYDROLASE / Membrane protein / protein complex / pH regulation
Function / homology
Function and homology information


trans-Golgi network transport vesicle membrane / proton-transporting V-type ATPase complex assembly / plant-type cell wall biogenesis / proton-transporting two-sector ATPase complex / unidimensional cell growth / glucose mediated signaling pathway / plant-type vacuole membrane / proton-transporting V-type ATPase, V1 domain / proton-transporting two-sector ATPase complex, catalytic domain / lysosomal lumen acidification ...trans-Golgi network transport vesicle membrane / proton-transporting V-type ATPase complex assembly / plant-type cell wall biogenesis / proton-transporting two-sector ATPase complex / unidimensional cell growth / glucose mediated signaling pathway / plant-type vacuole membrane / proton-transporting V-type ATPase, V1 domain / proton-transporting two-sector ATPase complex, catalytic domain / lysosomal lumen acidification / pollen development / proton-transporting V-type ATPase, V0 domain / plant-type cell wall / embryo development ending in seed dormancy / proton-transporting V-type ATPase complex / vacuolar proton-transporting V-type ATPase, V1 domain / vacuolar transport / vacuolar proton-transporting V-type ATPase, V0 domain / negative regulation of actin filament depolymerization / vacuolar proton-transporting V-type ATPase complex / plasmodesma / plant-type vacuole / chloroplast envelope / vacuolar acidification / actin filament capping / vacuole / vacuolar membrane / Golgi organization / proton-transporting ATPase activity, rotational mechanism / actin filament bundle assembly / H+-transporting two-sector ATPase / ATP metabolic process / response to cold / proton-transporting ATP synthase activity, rotational mechanism / proton transmembrane transport / trans-Golgi network membrane / trans-Golgi network / chloroplast / cytoplasmic stress granule / cytosolic ribosome / actin filament binding / ATPase binding / protease binding / endosome / structural constituent of ribosome / Golgi membrane / regulation of transcription by RNA polymerase II / endoplasmic reticulum membrane / Golgi apparatus / ATP hydrolysis activity / protein-containing complex / mitochondrion / extracellular region / ATP binding / membrane / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
: / Domain of unknown function (DUF7794) / TLDc domain / TLDc domain / TLDc domain profile. / domain in TBC and LysM domain containing proteins / ATPase, V1 complex, subunit H / ATPase, V1 complex, subunit H, C-terminal / ATPase, V1 complex, subunit H, C-terminal domain superfamily / V-ATPase subunit H ...: / Domain of unknown function (DUF7794) / TLDc domain / TLDc domain / TLDc domain profile. / domain in TBC and LysM domain containing proteins / ATPase, V1 complex, subunit H / ATPase, V1 complex, subunit H, C-terminal / ATPase, V1 complex, subunit H, C-terminal domain superfamily / V-ATPase subunit H / V-ATPase subunit H / ATPase, V1 complex, subunit A / ATPase, V1 complex, subunit C / Vacuolar ATP synthase subunit C superfamily / V-ATPase subunit C / Vacuolar (H+)-ATPase G subunit / V-type proton ATPase subunit S1/VOA1, transmembrane domain / Vacuolar (H+)-ATPase G subunit / V0 complex accessory subunit Ac45/VOA1 transmembrane domain / ATPase, V1 complex, subunit B / ATPase, V1 complex, subunit F, eukaryotic / ATPase, V0 complex, subunit e1/e2 / ATP synthase subunit H / ATPase, V0 complex, subunit d / V-ATPase proteolipid subunit C, eukaryotic / ATPase, V0 complex, subunit 116kDa, eukaryotic / ATPase, V0 complex, c/d subunit / V-type ATPase subunit C/d / V-type ATP synthase subunit c/d subunit superfamily / V-type ATP synthase c/d subunit, domain 3 superfamily / ATP synthase (C/AC39) subunit / V-ATPase proteolipid subunit / V-type ATPase, V0 complex, 116kDa subunit family / V-type ATPase 116kDa subunit family / V-type ATPase subunit E / V-type ATPase subunit E, C-terminal domain superfamily / ATP synthase (E/31 kDa) subunit / ATPase, V1 complex, subunit D / ATPase, V1 complex, subunit F / ATPase, V1 complex, subunit F superfamily / ATP synthase subunit D / ATP synthase (F/14-kDa) subunit / V-type ATP synthase regulatory subunit B/beta / V-type ATP synthase catalytic alpha chain / ATPsynthase alpha/beta subunit, N-terminal extension / ATPsynthase alpha/beta subunit barrel-sandwich domain / V-ATPase proteolipid subunit C-like domain / F/V-ATP synthase subunit C superfamily / ATP synthase subunit C / : / ATPase, F1/V1 complex, beta/alpha subunit, C-terminal / C-terminal domain of V and A type ATP synthase / ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain superfamily / ATP synthase subunit alpha, N-terminal domain-like superfamily / ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain / ATP synthase alpha/beta family, beta-barrel domain / ATPase, alpha/beta subunit, nucleotide-binding domain, active site / ATP synthase alpha and beta subunits signature. / ATPase, F1/V1/A1 complex, alpha/beta subunit, nucleotide-binding domain / ATP synthase alpha/beta family, nucleotide-binding domain / Armadillo-like helical / Armadillo-type fold / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / V-type proton ATPase catalytic subunit A / V-type proton ATPase subunit G1 / V-type proton ATPase subunit c1 / V-type proton ATPase subunit B1 / V-type proton ATPase subunit E1 / V-type proton ATPase subunit a1 / Uncharacterized protein At3g13410 / TLD-domain containing nucleolar protein / V-type proton ATPase subunit d1 ...ADENOSINE-5'-DIPHOSPHATE / V-type proton ATPase catalytic subunit A / V-type proton ATPase subunit G1 / V-type proton ATPase subunit c1 / V-type proton ATPase subunit B1 / V-type proton ATPase subunit E1 / V-type proton ATPase subunit a1 / Uncharacterized protein At3g13410 / TLD-domain containing nucleolar protein / V-type proton ATPase subunit d1 / V-type proton ATPase subunit H / V-type proton ATPase subunit C / V-type proton ATPase subunit e2 / V-type proton ATPase subunit c''1 / V-type proton ATPase subunit D / V-type proton ATPase subunit F / AT3g24160/MUJ8_16
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.3 Å
AuthorsKhamina, M. / Rubinstein, J.L.
Funding support Canada, Germany, 2items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)PJT195707 Canada
German Research Foundation (DFG)CRC1101 Germany
CitationJournal: To Be Published
Title: Cryo-EM structure of the Arabidopsis thaliana V-type ATPase
Authors: Khamina, M. / Wunsch, N. / Lupanga, U. / Fink, F. / Wang, H. / Schulze, W.X. / Schumacher, K. / Rubinstein, J.L.
History
DepositionJun 26, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 9, 2026Provider: repository / Type: Initial release
Revision 1.0Sep 9, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
T: TLD-domain containing nucleolar protein OXR5
a: V-type proton ATPase subunit a1
F: V-type proton ATPase subunit B1
G: V-type proton ATPase subunit E1
H: V-type proton ATPase subunit G1
I: V-type proton ATPase subunit E1
J: V-type proton ATPase subunit G1
K: V-type proton ATPase subunit E1
L: V-type proton ATPase subunit G1
M: V-type proton ATPase subunit D
N: V-type proton ATPase subunit F
P: V-type proton ATPase subunit H
b: V-type proton ATPase subunit AP1 fragment
c: V-type proton ATPase subunit c''1
d: V-type proton ATPase subunit d1
e: V-type proton ATPase subunit e2
g: V-type proton ATPase subunit c1
h: V-type proton ATPase subunit c1
i: V-type proton ATPase subunit c1
j: V-type proton ATPase subunit c1
k: V-type proton ATPase subunit c1
l: V-type proton ATPase subunit c1
m: V-type proton ATPase subunit c1
n: V-type proton ATPase subunit c1
o: V-type proton ATPase subunit c1
r: V-type proton ATPase subunit AP2 fragment
C: V-type proton ATPase catalytic subunit A
E: V-type proton ATPase catalytic subunit A
D: V-type proton ATPase subunit B1
O: V-type proton ATPase subunit C
B: V-type proton ATPase subunit B1
A: V-type proton ATPase catalytic subunit A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,065,35434
Polymers1,064,90232
Non-polymers4522
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Protein , 2 types, 4 molecules TCEA

#1: Protein TLD-domain containing nucleolar protein OXR5


Mass: 59973.324 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9FKA3
#15: Protein V-type proton ATPase catalytic subunit A / V-ATPase subunit A / V-ATPase 69 kDa subunit / Vacuolar H(+)-ATPase subunit A / Vacuolar proton ...V-ATPase subunit A / V-ATPase 69 kDa subunit / Vacuolar H(+)-ATPase subunit A / Vacuolar proton pump subunit alpha


Mass: 68884.234 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress)
References: UniProt: O23654, H+-transporting two-sector ATPase

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V-type proton ATPase subunit ... , 14 types, 28 molecules aFDBGIKHJLMNPbcdeghijklmnorO

#2: Protein V-type proton ATPase subunit a1 / V-ATPase subunit a1 / V-type proton ATPase 95 kDa subunit a isoform 1 / V-ATPase 95 kDa isoform a1 ...V-ATPase subunit a1 / V-type proton ATPase 95 kDa subunit a isoform 1 / V-ATPase 95 kDa isoform a1 / Vacuolar H(+)-ATPase subunit a isoform 1 / Vacuolar proton pump subunit a1 / Vacuolar proton translocating ATPase 95 kDa subunit a isoform 1


Mass: 93512.727 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q8RWZ7
#3: Protein V-type proton ATPase subunit B1 / V-ATPase subunit B1 / V-ATPase 57 kDa subunit / Vacuolar H(+)-ATPase subunit B isoform 1 / Vacuolar ...V-ATPase subunit B1 / V-ATPase 57 kDa subunit / Vacuolar H(+)-ATPase subunit B isoform 1 / Vacuolar proton pump subunit B1


Mass: 54164.352 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: P11574
#4: Protein V-type proton ATPase subunit E1 / V-ATPase subunit E1 / Protein EMBRYO DEFECTIVE 2448 / Vacuolar H(+)-ATPase subunit E isoform 1 / ...V-ATPase subunit E1 / Protein EMBRYO DEFECTIVE 2448 / Vacuolar H(+)-ATPase subunit E isoform 1 / Vacuolar proton pump subunit E1


Mass: 26101.053 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q39258
#5: Protein V-type proton ATPase subunit G1 / V-ATPase subunit G1 / Vacuolar H(+)-ATPase subunit G isoform 1 / Vacuolar proton pump subunit G1


Mass: 12416.915 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: O82628
#6: Protein V-type proton ATPase subunit D / V-ATPase subunit D / Vacuolar H(+)-ATPase subunit D / Vacuolar proton pump subunit D


Mass: 29104.756 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9XGM1
#7: Protein V-type proton ATPase subunit F / V-ATPase subunit F / V-ATPase 14 kDa subunit / Vacuolar H(+)-ATPase subunit F / Vacuolar proton pump subunit F


Mass: 14276.354 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9ZQX4
#8: Protein V-type proton ATPase subunit H / V-ATPase subunit H / Vacuolar H(+)-ATPase subunit H / Vacuolar proton pump subunit H


Mass: 50346.262 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9LX65
#9: Protein V-type proton ATPase subunit AP1 fragment


Mass: 35015.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q93WB8
#10: Protein V-type proton ATPase subunit c''1 / V-ATPase subunit c''1 / Vacuolar H(+)-ATPase subunit c'' isoform 1 / Vacuolar proton pump subunit c''1


Mass: 18383.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9SZY7
#11: Protein V-type proton ATPase subunit d1 / V-ATPase subunit d1 / Vacuolar H(+)-ATPase subunit d isoform 1 / Vacuolar proton pump subunit d1


Mass: 40835.688 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9LJI5
#12: Protein V-type proton ATPase subunit e2 / V-ATPase subunit e2 / Vacuolar H(+)-ATPase subunit e isoform 2 / Vacuolar proton pump subunit e2


Mass: 7688.377 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9SZ13
#13: Protein
V-type proton ATPase subunit c1 / V-ATPase subunit c1 / V-type proton ATPase 16 kDa proteolipid subunit c1 / V-ATPase 16 kDa ...V-ATPase subunit c1 / V-type proton ATPase 16 kDa proteolipid subunit c1 / V-ATPase 16 kDa proteolipid subunit c1 / Vacuolar H(+)-ATPase subunit c isoform 1 / Vacuolar proton pump 16 kDa proteolipid subunit c1 / Vacuolar proton pump subunit c1


Mass: 16581.588 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: P0DH92
#14: Protein V-type proton ATPase subunit AP2 fragment / Putative type 1 membrane protein / Type 1 membrane protein / putative


Mass: 39164.426 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9ZSJ7
#16: Protein V-type proton ATPase subunit C / V-ATPase subunit C / Vacuolar H(+)-ATPase subunit C / Vacuolar proton pump subunit C


Mass: 42667.199 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9SDS7

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Non-polymers , 2 types, 2 molecules

#17: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#18: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Arabidopsis V-ATPase State 1 / Type: COMPLEX / Entity ID: #1-#16 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Buffer solutionpH: 7
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER/RHODIUM / Grid mesh size: 400 divisions/in. / Grid type: Homemade
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 130000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: TFS FALCON 4i (4k x 4k) / Num. of real images: 7681
EM imaging opticsEnergyfilter name: TFS Selectris X / Energyfilter slit width: 10 eV

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.21.1_5286model refinement
5cryoSPARCCTF correction
10cryoSPARCinitial Euler assignment
11cryoSPARCfinal Euler assignment
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 190490
3D reconstructionResolution: 4.3 Å / Resolution method: DIFFRACTION PATTERN/LAYERLINES / Num. of particles: 5323 / Symmetry type: POINT
RefinementHighest resolution: 4.3 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00364081
ELECTRON MICROSCOPYf_angle_d0.5786692
ELECTRON MICROSCOPYf_dihedral_angle_d12.26723779
ELECTRON MICROSCOPYf_chiral_restr0.049951
ELECTRON MICROSCOPYf_plane_restr0.00511115

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