[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 insights into toxicant export mediated by ABCC2 in Arabidopsis thaliana.
Journal, issue, pagesNat Commun, Vol. 16, Issue 1, Page 11554, Year 2025
Publish dateDec 22, 2025
AuthorsXuan Qiu / Zhisen Yang / Yongxiang Gao / Linfeng Sun / Xin Liu /
PubMed AbstractPlants are highly vulnerable to damage from environmental pollutants, making detoxification mechanisms essential for sustaining growth and development. ABCC2 in Arabidopsis thaliana (AtABCC2) plays a ...Plants are highly vulnerable to damage from environmental pollutants, making detoxification mechanisms essential for sustaining growth and development. ABCC2 in Arabidopsis thaliana (AtABCC2) plays a critical role in detoxification by exporting diverse toxic compounds. Here, we report the structures of AtABCC2 in three distinct states: substrate-free, bound to the substrate S-(2,4-dinitrophenyl)glutathione (DNP-GS), and bound to ATP. Both monomeric and dimeric forms of AtABCC2 are observed. Unlike other dimeric ABCC homologs, AtABCC2 features a dimer interface mediated by its transmembrane domains. DNP-GS occupies an amphipathic cavity formed by the transmembrane domains. ATP binding drives the conformational changes in each protomer which bring the transmembrane and nucleotide-binding domains closer together, transitioning the transporter from a cytosolic-facing to an occluded state. Together, these findings advance our understanding of the molecular basis of substrate binding and transport by AtABCC2, and shed light on plant detoxification mechanisms.
External linksNat Commun / PubMed:41430060 / PubMed Central
MethodsEM (single particle)
Resolution3.42 - 4.2 Å
Structure data

63111

9li5

EMDB-63111, PDB-9li5:
Structure of the wild-type ABCC2 in Arabidopsis thaliana in the apo state
Method: EM (single particle) / Resolution: 3.9 Å

63112

9li6

EMDB-63112, PDB-9li6:
Structure of ABCC2(E1404Q) in Arabidopsis thaliana in the DNP-GS bound state
Method: EM (single particle) / Resolution: 3.49 Å

63113

9li7

EMDB-63113, PDB-9li7:
Structure of ABCC2(E1404Q) in Arabidopsis thaliana in the apo state
Method: EM (single particle) / Resolution: 3.54 Å

63114

9li9

EMDB-63114, PDB-9li9:
Structure of ABCC2(E1404Q) in Arabidopsis thaliana in the ATP bound state
Method: EM (single particle) / Resolution: 3.42 Å

65934

9wfp

EMDB-65934, PDB-9wfp:
Structure of ABCC2(E1404Q) monomer in Arabidopsis thaliana in the DNP-GS bound state
Method: EM (single particle) / Resolution: 4.1 Å

65935

9wfq

EMDB-65935, PDB-9wfq:
Structure of the wild-type ABCC2 dimer in Arabidopsis thaliana in the apo state
Method: EM (single particle) / Resolution: 4.2 Å

Chemicals

ChemComp-GDN:
GLUTATHIONE S-(2,4 DINITROBENZENE)

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

ChemComp-MG:
Unknown entry

Source
  • arabidopsis thaliana (thale cress)
KeywordsTRANSPORT PROTEIN / Plant detoxification effect / Transporter / ABCC2 protein / PROTEIN TRANSPORT

+
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