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- EMDB-65299: Structure of the wild-type CAX1 in Arabidopsis thaliana in the ap... -

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Basic information

Entry
Database: EMDB / ID: EMD-65299
TitleStructure of the wild-type 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 / 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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsSun L / Wang K
Funding support China, 1 items
OrganizationGrant numberCountry
National Science Foundation (NSF, China) China
CitationJournal: To Be Published
Title: Structure of the wild-type CAX1 in Arabidopsis thaliana in the apo state
Authors: Sun L / Wang K
History
DepositionJul 8, 2025-
Header (metadata) releaseSep 3, 2025-
Map releaseSep 3, 2025-
UpdateSep 3, 2025-
Current statusSep 3, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_65299.png

Downloads & links

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Map

FileDownload / File: emd_65299.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
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

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.4
Minimum - Maximum-1.5083526 - 2.3863516
Average (Standard dev.)0.00006576464 (±0.05810553)
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_65299_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_65299_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_65299_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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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: 51.209371 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MAGIVTEPWS VAENGNPSIT AKGSSRELRL GRTAHNMSSS SLRKKSDLRV IQKVPYKGLK DFLSNLQEVI LGTKLAILFP AIPAAIICT YCGVSQPWIF GLSLLGLTPL AERVSFLTEQ LAFYTGPTLG GLLNATCGNA TELIIAILAL TNNKVAVVKY S LLGSILSN ...String:
MAGIVTEPWS VAENGNPSIT AKGSSRELRL GRTAHNMSSS SLRKKSDLRV 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: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 82149
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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