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

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Basic information

Entry
Database: PDB / ID: 9vsd
TitleStructure of the phosphomimetic mutant CAX1 in Arabidopsis thaliana in the apo 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 / intracellular zinc ion homeostasis ...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 / intracellular zinc ion homeostasis / vacuole / vacuolar membrane / monoatomic cation transport / response to salt stress / calcium ion transmembrane transport / 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: 3.4 Å
AuthorsSun, L. / Wang, K.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, China) China
CitationJournal: Nat Plants / Year: 2025
Title: Structural basis of CAX1 autoinhibition by its amino-terminal domain in Arabidopsis thaliana.
Authors: Kun Wang / Chunhui Ma / Guanglin Chen / Zhisen Yang / Yongxiang Gao / Zhiyong Zhang / Xin Liu / Linfeng Sun /
Abstract: Calcium homeostasis is tightly regulated due to the essential roles of calcium ions (Ca) in various cellular processes. CAX1 in Arabidopsis thaliana (AtCAX1) serves as a Ca/H exchanger transporting ...Calcium homeostasis is tightly regulated due to the essential roles of calcium ions (Ca) in various cellular processes. CAX1 in Arabidopsis thaliana (AtCAX1) serves as a Ca/H exchanger transporting excess cytosolic Ca into the vacuole, which is modulated by kinase phosphorylation in response to diverse signals. However, the regulatory mechanism remains unclear. Here we present the structures of wild-type AtCAX1 in an inactivated state and a phosphomimetic mutant in an activated state. In the wild-type structure, the amino-terminal region forms an α-helix that blocks the transport tunnel, thus inhibiting its transport activity. In contrast, in the phosphomimetic mutant structure, this blocking helix is released from the tunnel, leading to AtCAX1 activation. Conformational changes are also observed in the transmembrane domain. Together, these findings provide insights into the transport mechanism of the Ca/H exchangers and set up a basis for future studies of the regulation of calcium homeostasis in plants.
History
DepositionJul 8, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Sep 3, 2025Provider: 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


Theoretical massNumber of molelcules
Total (without water)153,9643
Polymers153,9643
Non-polymers00
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
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: all / 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: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 86386 / Symmetry type: POINT

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