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- EMDB-65301: Structure of the phosphomimetic mutant CAX1 in Arabidopsis thalia... -

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Basic information

Entry
Database: EMDB / ID: EMD-65301
TitleStructure of the phosphomimetic mutant CAX1 in Arabidopsis thaliana in the apo state
Map data
Sample
  • Complex: CAX1 trimer
    • Protein or peptide: Vacuolar cation/proton exchanger 1
KeywordsCalcium / Transporter / Proton / CAX1 / TRANSPORT PROTEIN
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsSun L / Wang K
Funding support China, 1 items
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, 2025-
Header (metadata) releaseSep 3, 2025-
Map releaseSep 3, 2025-
UpdateMar 18, 2026-
Current statusMar 18, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_65301.png

Downloads & links

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Map

FileDownload / File: emd_65301.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 256 pix.
= 281.6 Å		1.1 Å/pix.
x 256 pix.
= 281.6 Å		1.1 Å/pix.
x 256 pix.
= 281.6 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.4
Minimum - Maximum-1.2385015 - 1.7338096
Average (Standard dev.)-0.00050175743 (±0.039664853)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 281.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_65301_msk_1.map
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Half map: #2

Fileemd_65301_half_map_1.map
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Half map: #1

Fileemd_65301_half_map_2.map
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Sample components

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Entire : CAX1 trimer

EntireName: CAX1 trimer
Components
  • Complex: CAX1 trimer
    • Protein or peptide: Vacuolar cation/proton exchanger 1

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Supramolecule #1: CAX1 trimer

SupramoleculeName: CAX1 trimer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Arabidopsis thaliana (thale cress)

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Macromolecule #1: Vacuolar cation/proton exchanger 1

MacromoleculeName: Vacuolar cation/proton exchanger 1 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 51.32141 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MAGIVTEPWS VAENGNPSIT AKGSSRELRL GRTAHNMDDD DLRKKSDLRV IQKVPYKGLK DFLSNLQEVI LGTKLAILFP AIPAAIICT YCGVSQPWIF GLSLLGLTPL AERVSFLTEQ LAFYTGPTLG GLLNATCGNA TELIIAILAL TNNKVAVVKY S LLGSILSN ...String:
MAGIVTEPWS VAENGNPSIT AKGSSRELRL GRTAHNMDDD DLRKKSDLRV IQKVPYKGLK DFLSNLQEVI LGTKLAILFP AIPAAIICT YCGVSQPWIF GLSLLGLTPL AERVSFLTEQ LAFYTGPTLG GLLNATCGNA TELIIAILAL TNNKVAVVKY S LLGSILSN LLLVLGTSLF CGGIANIRRE QRFDRKQADV NFFLLLLGFL CHLLPLLVGY LKNGEASAAV LSDMQLSISR GF SIVMLIS YIAYLVFQLW THRQLFDAQE QEDEYDDDVE QETAVISFWS GFAWLVGMTL VIALLSEYVV ATIEEASDKW NLS VSFISI ILLPIVGNAA EHAGAVIFAF KNKLDISLGV ALGSATQIGL FVVPLTIIVA WILGINMDLN FGPLETGCLA VSII ITAFT LQDGSSHYMK GLVLLLCYFI IAICFFVDKL PQKQNAIHLG HQAMNNVVTA TGGGVFSSDY KDDDDK

UniProtKB: Vacuolar cation/proton exchanger 1

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 86386
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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