[English] 日本語
Yorodumi
- EMDB-65300: Structure of the phosphomimetic mutant CAX1 in Arabidopsis thalia... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-65300
TitleStructure of the phosphomimetic mutant CAX1 in Arabidopsis thaliana in the Calcium-bound state
Map data
Sample
  • Complex: CAX1 trimer
    • Protein or peptide: Vacuolar cation/proton exchanger 1
  • Ligand: CALCIUM ION
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: 3.2 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 phosphomimetic mutant CAX1 in Arabidopsis thaliana in the Calcium-bound 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

-
Structure visualization

Supplemental images

emd_65300.png

Downloads & links

-
Map

FileDownload / File: emd_65300.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-1.5880027 - 2.3945777
Average (Standard dev.)-0.00020961837 (±0.048956558)
SymmetrySpace group: 1
Details

EMDB XML:

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

-
Supplemental data

-
Mask #1

Fileemd_65300_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_65300_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_65300_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : CAX1 trimer

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

-
Supramolecule #1: CAX1 trimer

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

-
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

-
Macromolecule #2: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 2 / Number of copies: 3 / Formula: CA
Molecular weightTheoretical: 40.078 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

-
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

+
Image processing

CTF correctionType: NONE
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 101980
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more