[English] 日本語
Yorodumi
- EMDB-64489: influx carrier substrate bound form -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-64489
Titleinflux carrier substrate bound form
Map data
Sample
  • Organelle or cellular component: plant influx carrier hormone bound form
    • Protein or peptide: Auxin transporter protein 1
  • Ligand: (2,4-DICHLOROPHENOXY)ACETIC ACID
  • Ligand: SODIUM ION
Keywordshormone transporter / HORMONE
Function / homology
Function and homology information


root hair cell differentiation / auxin binding / root cap development / lateral root formation / auxin influx transmembrane transporter activity / positive gravitropism / establishment of planar polarity / auxin polar transport / auxin-activated signaling pathway / response to nematode ...root hair cell differentiation / auxin binding / root cap development / lateral root formation / auxin influx transmembrane transporter activity / positive gravitropism / establishment of planar polarity / auxin polar transport / auxin-activated signaling pathway / response to nematode / amino acid transmembrane transporter activity / symporter activity / endosome / cell surface / Golgi apparatus / plasma membrane
Similarity search - Function
Amino acid transporter, transmembrane domain / Transmembrane amino acid transporter protein
Similarity search - Domain/homology
Auxin transporter protein 1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.06 Å
AuthorsChen H / Jiang D
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Mol Plant / Year: 2025
Title: Structural basis of auxin recognition and transport by the plant influx carrier AUX1.
Authors: Huiwen Chen / Junping Fan / Cheng Chi / Jun Zhao / Di Wu / Xiaoguang Lei / Xing Wang Deng / Daohua Jiang /
Abstract: Auxin regulates numerous aspects of plant growth and development, featuring polar auxin transport mediated by auxin efflux and influx carriers. AUX1 is the major auxin importer that actively takes up ...Auxin regulates numerous aspects of plant growth and development, featuring polar auxin transport mediated by auxin efflux and influx carriers. AUX1 is the major auxin importer that actively takes up natural and synthetic auxins. However, the precise mechanisms underlying AUX1-mediated auxin recognition and transport remain elusive. Here, we present cryoelectron microscopy structures of Arabidopsis thaliana AUX1 in both apo and auxin-bound states, revealing the structural basis for auxin recognition. Structural analyses show that AUX1 assumes the LeuT-like fold in an inward-facing conformation and the auxin analog 2,4-D is recognized by polar residues located in the central cavity of AUX1. Furthermore, we identify a putative cation-binding site that contributes to stabilizing the inward-facing conformation. Interestingly, we reveal that His249 undergoes a substantial conformational shift, and its mutation completely abolishes transport activity, suggesting a crucial role for His249 in AUX1 gating. Collectively, this study provides a structural foundation for a deeper understanding of auxin influx by AUX1-like carriers.
History
DepositionMay 3, 2025-
Header (metadata) releaseDec 24, 2025-
Map releaseDec 24, 2025-
UpdateDec 24, 2025-
Current statusDec 24, 2025Processing site: PDBc / Status: Released

-
Structure visualization

Supplemental images

emd_64489.png

Downloads & links

-
Map

FileDownload / File: emd_64489.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 320 pix.
= 272. Å		0.85 Å/pix.
x 320 pix.
= 272. Å		0.85 Å/pix.
x 320 pix.
= 272. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.85 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-1.0284462 - 1.8945732
Average (Standard dev.)-0.0008112427 (±0.026557796)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 272.0 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #1

Fileemd_64489_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_64489_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : plant influx carrier hormone bound form

EntireName: plant influx carrier hormone bound form
Components
  • Organelle or cellular component: plant influx carrier hormone bound form
    • Protein or peptide: Auxin transporter protein 1
  • Ligand: (2,4-DICHLOROPHENOXY)ACETIC ACID
  • Ligand: SODIUM ION

-
Supramolecule #1: plant influx carrier hormone bound form

SupramoleculeName: plant influx carrier hormone bound form / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Arabidopsis thaliana (thale cress)

-
Macromolecule #1: Auxin transporter protein 1

MacromoleculeName: Auxin transporter protein 1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 54.10552 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MSEGVEAIVA NDNGTDQVNG NRTGKDNEEH DGSTGSNLSN FLWHGGSVWD AWFSCASNQV AQVLLTLPYS FSQLGMLSGI VLQIFYGLL GSWTAYLISV LYVEYRARKE KEGKSFKNHV IQWFEVLDGL LGSYWKALGL AFNCTFLLFG SVIQLIACAS N IYYINDHL ...String:
MSEGVEAIVA NDNGTDQVNG NRTGKDNEEH DGSTGSNLSN FLWHGGSVWD AWFSCASNQV AQVLLTLPYS FSQLGMLSGI VLQIFYGLL GSWTAYLISV LYVEYRARKE KEGKSFKNHV IQWFEVLDGL LGSYWKALGL AFNCTFLLFG SVIQLIACAS N IYYINDHL DKRTWTYIFG ACCATTVFIP SFHNYRIWSF LGLGMTTYTA WYLAIASIIH GQAEGVKHSG PTKLVLYFTG AT NILYTFG GHAVTVEIMH AMWKPQKFKY IYLMATLYVF TLTIPSAAAV YWAFGDALLD HSNAFSLMPK NAWRDAAVIL MLI HQFITF GFACTPLYFV WEKVIGMHDT KSICLRALAR LPVVIPIWFL AIIFPFFGPI NSAVGALLVS FTVYIIPSLA HMLT YRSAS ARQNAAEKPP FFMPSWTAMY VLNAFVVVWV LIVGFGFGGW ASVTNFVRQV DTFGLFAKCY QCKPAAAAAH APVSA LHHR L

UniProtKB: Auxin transporter protein 1

-
Macromolecule #2: (2,4-DICHLOROPHENOXY)ACETIC ACID

MacromoleculeName: (2,4-DICHLOROPHENOXY)ACETIC ACID / type: ligand / ID: 2 / Number of copies: 1 / Formula: CFA
Molecular weightTheoretical: 221.037 Da
Chemical component information

ChemComp-CFA:
(2,4-DICHLOROPHENOXY)ACETIC ACID

-
Macromolecule #3: SODIUM ION

MacromoleculeName: SODIUM ION / type: ligand / ID: 3 / Number of copies: 1
Molecular weightTheoretical: 22.99 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration10 mg/mL
BufferpH: 7.4
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeTFS TITAN THEMIS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.06 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 129741
Initial angle assignmentType: RANDOM ASSIGNMENT
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