[English] 日本語
Yorodumi Papers
- Database of articles cited by EMDB/PDB/SASBDB data -

+
Search query

Keywords
Structure methods
Author
Journal
IF

-
Structure paper

TitleStructural basis of CAX1 autoinhibition by its amino-terminal domain in Arabidopsis thaliana.
Journal, issue, pagesNat Plants, Vol. 11, Issue 10, Page 2072-2083, Year 2025
Publish dateSep 2, 2025
AuthorsKun Wang / Chunhui Ma / Guanglin Chen / Zhisen Yang / Yongxiang Gao / Zhiyong Zhang / Xin Liu / Linfeng Sun /
PubMed AbstractCalcium 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.
External linksNat Plants / PubMed:40897811
MethodsEM (single particle)
Resolution3.4 Å
Structure data

EMDB-65301, PDB-9vsd:
Structure of the phosphomimetic mutant CAX1 in Arabidopsis thaliana in the apo state
Method: EM (single particle) / Resolution: 3.4 Å

Source
  • arabidopsis thaliana (thale cress)
KeywordsTRANSPORT PROTEIN / Calcium;Transporter;Proton;CAX1

+
About Yorodumi Papers

-
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 Papers

Database of articles cited by EMDB/PDB/SASBDB data

  • Database of articles cited by EMDB, PDB, and SASBDB entries
  • Using PubMed data

Related info.:EMDB / PDB / SASBDB / Yorodumi / EMN Papers / Changes in new EM Navigator and Yorodumi

Read more