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- PDB-9vsc: Structure of the phosphomimetic mutant CAX1 in Arabidopsis thalia... -

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Basic information

Entry
Database: PDB / ID: 9vsc
TitleStructure of the phosphomimetic mutant CAX1 in Arabidopsis thaliana in the Calcium-bound state
ComponentsVacuolar cation/proton exchanger 1
KeywordsTRANSPORT PROTEIN / Calcium / Transporter / Proton / CAX1
Function / homology
Function and homology information


calcium:proton antiporter complex / calcium:proton antiporter activity / lithium ion transport / plant-type vacuole membrane / cold acclimation / intracellular manganese ion homeostasis / regulation of stomatal movement / phosphate ion homeostasis / plant-type vacuole / vacuole ...calcium:proton antiporter complex / calcium:proton antiporter activity / lithium ion transport / plant-type vacuole membrane / cold acclimation / intracellular manganese ion homeostasis / regulation of stomatal movement / phosphate ion homeostasis / plant-type vacuole / vacuole / intracellular zinc ion homeostasis / monoatomic cation transport / response to salt stress / intracellular calcium ion homeostasis / calcium ion transport
Similarity search - Function
Calcium/proton exchanger / Calcium/proton exchanger CAX-like / Sodium/calcium exchanger membrane region / NCX, central ion-binding domain superfamily / Sodium/calcium exchanger protein
Similarity search - Domain/homology
Vacuolar cation/proton exchanger 1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsSun, L. / Wang, K.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, China) China
CitationJournal: To Be Published
Title: Structure of the phosphomimetic mutant CAX1 in Arabidopsis thaliana in the Calcium-bound state
Authors: Sun, L. / Wang, K.
History
DepositionJul 8, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Sep 3, 2025Provider: repository / Type: Initial release
Revision 1.0Sep 3, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Sep 3, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
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Revision 1.0Sep 3, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Sep 3, 2025Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Sep 3, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Vacuolar cation/proton exchanger 1
B: Vacuolar cation/proton exchanger 1
C: Vacuolar cation/proton exchanger 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)154,0846
Polymers153,9643
Non-polymers1203
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

#1: Protein Vacuolar cation/proton exchanger 1 / Ca(2+)/H(+) antiporter CAX1 / Ca(2+)/H(+) exchanger 1 / Protein CATION EXCHANGER 1 / Protein RARE ...Ca(2+)/H(+) antiporter CAX1 / Ca(2+)/H(+) exchanger 1 / Protein CATION EXCHANGER 1 / Protein RARE COLD INDUCIBLE 4


Mass: 51321.410 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: CAX1, RCI4, At2g38170, F16M14.10 / Production host: Homo sapiens (human) / References: UniProt: Q39253
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
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: CAX1 trimer / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
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: OTHER
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.13_2998:model refinement
13cryoSPARC3D reconstruction
CTF correctionType: NONE
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 101980 / Symmetry type: POINT

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