[English] 日本語
Yorodumi
- EMDB-62438: IAA bound mTAUT -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-62438
TitleIAA bound mTAUT
Map data
Sample
  • Complex: TAUT
    • Protein or peptide: heavy chain of 9D5 fab
    • Protein or peptide: Sodium- and chloride-dependent taurine transporter
    • Protein or peptide: light chain of 9D5 fab
  • Ligand: CHLORIDE ION
  • Ligand: 2H-IMIDAZOL-4-YLACETIC ACID
  • Ligand: SODIUM ION
KeywordsTransporter / Taurine / Chlorine / Sodium / MEMBRANE PROTEIN/IMMUNE SYSTEM / MEMBRANE PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


Na+/Cl- dependent neurotransmitter transporters / Amino acid transport across the plasma membrane / alanine transmembrane transporter activity / taurine:sodium symporter activity / gamma-aminobutyric acid:sodium:chloride symporter activity / amino acid:sodium symporter activity / amino acid import across plasma membrane / taurine transmembrane transport / neurotransmitter transport / microvillus membrane ...Na+/Cl- dependent neurotransmitter transporters / Amino acid transport across the plasma membrane / alanine transmembrane transporter activity / taurine:sodium symporter activity / gamma-aminobutyric acid:sodium:chloride symporter activity / amino acid:sodium symporter activity / amino acid import across plasma membrane / taurine transmembrane transport / neurotransmitter transport / microvillus membrane / positive regulation of cell differentiation / modulation of chemical synaptic transmission / GABA-ergic synapse / basolateral plasma membrane / postsynaptic membrane / apical plasma membrane / plasma membrane
Similarity search - Function
Sodium:neurotransmitter symporter, taurine / Sodium:neurotransmitter symporter family signature 2. / Sodium:neurotransmitter symporter family signature 1. / Sodium:neurotransmitter symporter / Sodium:neurotransmitter symporter superfamily / Sodium:neurotransmitter symporter family / Sodium:neurotransmitter symporter family profile.
Similarity search - Domain/homology
Sodium- and chloride-dependent taurine transporter
Similarity search - Component
Biological speciesMus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsShe J / Wang M / He J
Funding support China, 4 items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2021YFF0600801 China
National Natural Science Foundation of China (NSFC)32071201 China
National Natural Science Foundation of China (NSFC)32100967 China
Center for Advanced Interdisciplinary Science and Biomedicine of IHMQYPY20220009 China
CitationJournal: Proc Natl Acad Sci U S A / Year: 2025
Title: Molecular basis for substrate recognition and transport of mammalian taurine transporters.
Authors: Mingxing Wang / Jin He / Qianwen Cai / Shen-Ao Zhang / Ji She /
Abstract: The taurine transporter (TAUT) mediates cellular taurine uptake, playing a critical role in human health and longevity. In this study, we present cryogenic electron microscopy structures of both ...The taurine transporter (TAUT) mediates cellular taurine uptake, playing a critical role in human health and longevity. In this study, we present cryogenic electron microscopy structures of both mouse and human TAUT in various conformational states. The taurine-bound, occluded forms of mouse and human TAUT reveal the substrate binding pocket and the ion binding sites. The amino group of taurine interacts with Glu406 at the binding site, constituting a key structural feature determining substrate preference. While both imidazole acetic acid and guanidinoethyl sulfonate (GES) inhibit TAUT by competing with taurine for the binding site, GES also functions as a substrate of TAUT. Moreover, mouse TAUT is captured in an inward-open apo conformation, where the tilted movement of transmembrane helix (TM) 1a opens the intracellular gate. Notably, TM6 exhibits two distinct conformational states: the canonical form consisting of two half-helices and a continuous straight helix. In the latter conformation, TM6 partially occupies the substrate binding site, likely promoting taurine release. Together, our findings provide critical insights into the molecular mechanisms by which TAUT recognizes and transports taurine.
History
DepositionNov 16, 2024-
Header (metadata) releaseJul 2, 2025-
Map releaseJul 2, 2025-
UpdateJul 16, 2025-
Current statusJul 16, 2025Processing site: PDBc / Status: Released

-
Structure visualization

Supplemental images

emd_62438.png

Downloads & links

-
Map

FileDownload / File: emd_62438.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 384 pix.
= 314.88 Å		0.82 Å/pix.
x 384 pix.
= 314.88 Å		0.82 Å/pix.
x 384 pix.
= 314.88 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.82 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-1.5396224 - 2.0128198
Average (Standard dev.)-0.00040797726 (±0.025335263)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 314.88 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #2

Fileemd_62438_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_62438_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : TAUT

EntireName: TAUT
Components
  • Complex: TAUT
    • Protein or peptide: heavy chain of 9D5 fab
    • Protein or peptide: Sodium- and chloride-dependent taurine transporter
    • Protein or peptide: light chain of 9D5 fab
  • Ligand: CHLORIDE ION
  • Ligand: 2H-IMIDAZOL-4-YLACETIC ACID
  • Ligand: SODIUM ION

-
Supramolecule #1: TAUT

SupramoleculeName: TAUT / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Mus musculus (house mouse)

-
Macromolecule #1: heavy chain of 9D5 fab

MacromoleculeName: heavy chain of 9D5 fab / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 13.138654 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString:
EVQLVESGGG LVKPGGSLKL SCAASGFTFS SYAMSWVRQS PEKRLEWVAE ISSGGRYIYY SDTVTGRFTI SRDNARNILH LEMSSLRSE DTAMYYCARG EVRQRGFDYW GQGTTLTVS

-
Macromolecule #2: Sodium- and chloride-dependent taurine transporter

MacromoleculeName: Sodium- and chloride-dependent taurine transporter / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 70.051891 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MATKEKLQCL KDFHKDILKP SPGKSPGTRP EDEADGKPPQ REKWSSKIDF VLSVAGGFVG LGNVWRFPYL CYKNGGGAFL IPYFIFLFG SGLPVFFLEV IIGQYTSEGG ITCWEKICPL FSGIGYASIV IVSLLNVYYI VILAWATYYL FHSFQKDLPW A HCNHSWNT ...String:
MATKEKLQCL KDFHKDILKP SPGKSPGTRP EDEADGKPPQ REKWSSKIDF VLSVAGGFVG LGNVWRFPYL CYKNGGGAFL IPYFIFLFG SGLPVFFLEV IIGQYTSEGG ITCWEKICPL FSGIGYASIV IVSLLNVYYI VILAWATYYL FHSFQKDLPW A HCNHSWNT PQCMEDTLRR NESHWVSLST ANFTSPVIEF WERNVLSLSS GIDNPGSLKW DLALCLLLVW LVCFFCIWKG VR STGKVVY FTATFPFAML LVLLVRGLTL PGAGEGIKFY LYPDISRLGD PQVWIDAGTQ IFFSYAICLG AMTSLGSYNK YKY NSYRDC MLLGCLNSGT SFVSGFAIFS ILGFMAQEQG VDIADVAESG PGLAFIAYPK AVTMMPLPTF WSILFFIMLL LLGL DSQFV EVEGQITSLV DLYPSFLRKG YRREIFIAIL CSISYLLGLT MVTEGGMYVF QLFDYYAASG VCLLWVAFFE CFVIA WIYG VNRFSEDIRD MIGYRPGPWM KYSWAVITPA LCVGCFVFSL VKYVPLTYNK VYRYPDWAIG LGWGLALSSM LCIPLV IVI LLCRTEGPLR VRIKYLITPR EPNRWAVERE GATPFHSRVT LMNGALMKPS HVIVETMM

UniProtKB: Sodium- and chloride-dependent taurine transporter

-
Macromolecule #3: light chain of 9D5 fab

MacromoleculeName: light chain of 9D5 fab / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 11.480681 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString:
ENVLTQSPAI MSTSPGEKVT MTCRASSSVG SSYLHWYQQK SGASPKLWIY STSNLASGVP ARFSGSGSGT SYSLTISSVE AEDAATYYC QQFSGYPLTF GSGTKLEMK

-
Macromolecule #4: CHLORIDE ION

MacromoleculeName: CHLORIDE ION / type: ligand / ID: 4 / Number of copies: 1 / Formula: CL
Molecular weightTheoretical: 35.453 Da

-
Macromolecule #5: 2H-IMIDAZOL-4-YLACETIC ACID

MacromoleculeName: 2H-IMIDAZOL-4-YLACETIC ACID / type: ligand / ID: 5 / Number of copies: 1 / Formula: IZC
Molecular weightTheoretical: 126.113 Da
Chemical component information

ChemComp-IZC:
2H-IMIDAZOL-4-YLACETIC ACID

-
Macromolecule #6: SODIUM ION

MacromoleculeName: SODIUM ION / type: ligand / ID: 6 / Number of copies: 2
Molecular weightTheoretical: 22.99 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 (6k x 4k) / Average electron dose: 54.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.7 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: NONE
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 372774
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