[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 auxin recognition and efflux by Arabidopsis PIN1.
Journal, issue, pagesNature, Vol. 609, Issue 7927, Page 611-615, Year 2022
Publish dateAug 2, 2022
AuthorsZhisen Yang / Jing Xia / Jingjing Hong / Chenxi Zhang / Hong Wei / Wei Ying / Chunqiao Sun / Lianghanxiao Sun / Yanbo Mao / Yongxiang Gao / Shutang Tan / Jiří Friml / Dianfan Li / Xin Liu / Linfeng Sun /
PubMed AbstractPolar auxin transport is unique to plants and coordinates their growth and development. The PIN-FORMED (PIN) auxin transporters exhibit highly asymmetrical localizations at the plasma membrane and ...Polar auxin transport is unique to plants and coordinates their growth and development. The PIN-FORMED (PIN) auxin transporters exhibit highly asymmetrical localizations at the plasma membrane and drive polar auxin transport; however, their structures and transport mechanisms remain largely unknown. Here, we report three inward-facing conformation structures of Arabidopsis thaliana PIN1: the apo state, bound to the natural auxin indole-3-acetic acid (IAA), and in complex with the polar auxin transport inhibitor N-1-naphthylphthalamic acid (NPA). The transmembrane domain of PIN1 shares a conserved NhaA fold. In the substrate-bound structure, IAA is coordinated by both hydrophobic stacking and hydrogen bonding. NPA competes with IAA for the same site at the intracellular pocket, but with a much higher affinity. These findings inform our understanding of the substrate recognition and transport mechanisms of PINs and set up a framework for future research on directional auxin transport, one of the most crucial processes underlying plant development.
External linksNature / PubMed:35917925 / PubMed Central
MethodsEM (single particle)
Resolution3.1 - 3.3 Å
Structure data

EMDB-33691, PDB-7y9t:
Structure of the auxin exporter PIN1 in Arabidopsis thaliana in the apo state
Method: EM (single particle) / Resolution: 3.1 Å

EMDB-33692, PDB-7y9u:
Structure of the auxin exporter PIN1 in Arabidopsis thaliana in the NPA-bound state
Method: EM (single particle) / Resolution: 3.3 Å

EMDB-33693, PDB-7y9v:
Structure of the auxin exporter PIN1 in Arabidopsis thaliana in the IAA-bound state
Method: EM (single particle) / Resolution: 3.2 Å

Chemicals

ChemComp-E7O:
2-(naphthalen-1-ylcarbamoyl)benzoic acid

ChemComp-IAC:
1H-INDOL-3-YLACETIC ACID / hormone*YM

ChemComp-HOH:
WATER

Source
  • arabidopsis thaliana (thale cress)
  • escherichia coli (E. coli)
KeywordsTRANSPORT PROTEIN

+
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://pdbjlvh1.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