[English] 日本語
Yorodumi
- EMDB-62564: Structure of TauT in the apo state -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-62564
TitleStructure of TauT in the apo state
Map dataSharpened map of hTauT in the apo state
Sample
  • Complex: Sodium- and chloride-dependent taurine transporter
    • Protein or peptide: Sodium- and chloride-dependent taurine transporter
  • Ligand: CHLORIDE ION
  • Ligand: water
KeywordsTauT / SLC6A6 / taurine transporter / MEMBRANE PROTEIN
Function / homology
Function and homology information


taurine transmembrane transporter activity / alanine transmembrane transporter activity / gamma-aminobutyric acid transmembrane transporter activity / taurine:sodium symporter activity / import across plasma membrane / gamma-aminobutyric acid import / gamma-aminobutyric acid:sodium:chloride symporter activity / alanine transport / amino acid:sodium symporter activity / amino acid import across plasma membrane ...taurine transmembrane transporter activity / alanine transmembrane transporter activity / gamma-aminobutyric acid transmembrane transporter activity / taurine:sodium symporter activity / import across plasma membrane / gamma-aminobutyric acid import / gamma-aminobutyric acid:sodium:chloride symporter activity / alanine transport / amino acid:sodium symporter activity / amino acid import across plasma membrane / taurine transmembrane transport / Amino acid transport across the plasma membrane / amino acid transmembrane transporter activity / SLC-mediated transport of neurotransmitters / neurotransmitter transport / microvillus membrane / amino acid transport / transport across blood-brain barrier / sodium ion transmembrane transport / cell projection / positive regulation of cell differentiation / modulation of chemical synaptic transmission / GABA-ergic synapse / basolateral plasma membrane / postsynaptic membrane / apical plasma membrane / neuronal cell body / dendrite / 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 speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsYin YX / Lu YS / Ding D
Funding support China, 3 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)82030081 China
National Natural Science Foundation of China (NSFC)81874235 China
National Natural Science Foundation of China (NSFC)82173386 China
CitationJournal: Cell Rep / Year: 2025
Title: Structural determination of the human taurine transporter TauT reveals the mechanism of substrate and inhibitor recognition.
Authors: Yishuo Lu / Dian Ding / Hongyi Chen / Peijun Jiang / Juan Luo / Hui Shan / Guangxi Wang / Jianyuan Luo / Yuxin Yin /
Abstract: Taurine, a sulfur-containing amino acid, is vital for human health because of its antioxidant, anti-inflammatory, and osmoregulatory properties. Its homeostasis is maintained by the Na/Cl-dependent ...Taurine, a sulfur-containing amino acid, is vital for human health because of its antioxidant, anti-inflammatory, and osmoregulatory properties. Its homeostasis is maintained by the Na/Cl-dependent taurine transporter (TauT). Here, we present five atomic structures of human TauT: apo, taurine bound, and complexes with three taurine-mimetic inhibitors, including β-alanine, γ-aminobutyric acid (GABA), and guanidinoethyl sulfonate (GES). The structures of taurine-, β-alanine-, and GABA-bound human TauT (hTauT) in complex with NaCl adopt an occluded conformation, with ligands binding in a central pocket. With KCl, GES-bound hTauT adopts an inward-facing conformation, with two GES positioned along the substrate translocation pathway in a bipartite manner: one in the deep central cavity and the other precluding structural transition to the occluded state. The radioactive taurine uptake analyses clearly demonstrate the impact of residues on taurine recognition and inhibitor selection. These structures provide insights into the overall architecture, substrate coordination, and inhibitor recognition mechanism of TauT.
History
DepositionDec 2, 2024-
Header (metadata) releaseDec 3, 2025-
Map releaseDec 3, 2025-
UpdateDec 3, 2025-
Current statusDec 3, 2025Processing site: PDBc / Status: Released

-
Structure visualization

Supplemental images

emd_62564.png

Downloads & links

-
Map

FileDownload / File: emd_62564.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened map of hTauT in the apo state
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.67 Å/pix.
x 400 pix.
= 268. Å		0.67 Å/pix.
x 400 pix.
= 268. Å		0.67 Å/pix.
x 400 pix.
= 268. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.67 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.134
Minimum - Maximum-0.7816843 - 1.1535999
Average (Standard dev.)-0.00032113623 (±0.021077624)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 268.0 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Additional map: Map of hTauT in the apo state

Fileemd_62564_additional_1.map
AnnotationMap of hTauT in the apo state
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half-A map of hTauT in the apo state

Fileemd_62564_half_map_1.map
AnnotationHalf-A map of hTauT in the apo state
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half-B map of hTauT in the apo state

Fileemd_62564_half_map_2.map
AnnotationHalf-B map of hTauT in the apo state
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Sodium- and chloride-dependent taurine transporter

EntireName: Sodium- and chloride-dependent taurine transporter
Components
  • Complex: Sodium- and chloride-dependent taurine transporter
    • Protein or peptide: Sodium- and chloride-dependent taurine transporter
  • Ligand: CHLORIDE ION
  • Ligand: water

-
Supramolecule #1: Sodium- and chloride-dependent taurine transporter

SupramoleculeName: Sodium- and chloride-dependent taurine transporter / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 69.83 kDa/nm

-
Macromolecule #1: Sodium- and chloride-dependent taurine transporter

MacromoleculeName: Sodium- and chloride-dependent taurine transporter / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 69.881633 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MATKEKLQCL KDFHKDILKP SPGKSPGTRP EDEAEGKPPQ REKWSSKIDF VLSVAGGFVG LGNVWRFPYL CYKNGGGAFL IPYFIFLFG SGLPVFFLEI IIGQYTSEGG ITCWEKICPL FSGIGYASVV IVSLLNVYYI VILAWATYYL FQSFQKELPW A HCNHSWNT ...String:
MATKEKLQCL KDFHKDILKP SPGKSPGTRP EDEAEGKPPQ REKWSSKIDF VLSVAGGFVG LGNVWRFPYL CYKNGGGAFL IPYFIFLFG SGLPVFFLEI IIGQYTSEGG ITCWEKICPL FSGIGYASVV IVSLLNVYYI VILAWATYYL FQSFQKELPW A HCNHSWNT PHCMEDTMRK NKSVWITISS TNFTSPVIEF WERNVLSLSP GIDHPGSLKW DLALCLLLVW LVCFFCIWKG VR STGKVVY FTATFPFAML LVLLVRGLTL PGAGAGIKFY LYPDITRLED PQVWIDAGTQ IFFSYAICLG AMTSLGSYNK YKY NSYRDC MLLGCLNSGT SFVSGFAIFS ILGFMAQEQG VDIADVAESG PGLAFIAYPK AVTMMPLPTF WSILFFIMLL LLGL DSQFV EVEGQITSLV DLYPSFLRKG YRREIFIAFV CSISYLLGLT MVTEGGMYVF QLFDYYAASG VCLLWVAFFE CFVIA WIYG GDNLYDGIED MIGYRPGPWM KYSWAVITPV LCVGCFIFSL VKYVPLTYNK TYVYPNWAIG LGWSLALSSM LCVPLV IVI RLCQTEGPFL VRVKYLLTPR EPNRWAVERE GATPYNSRTV MNGALVKPTH IIVETMM

UniProtKB: Sodium- and chloride-dependent taurine transporter

-
Macromolecule #2: CHLORIDE ION

MacromoleculeName: CHLORIDE ION / type: ligand / ID: 2 / Number of copies: 1 / Formula: CL
Molecular weightTheoretical: 35.453 Da

-
Macromolecule #3: water

MacromoleculeName: water / type: ligand / ID: 3 / Number of copies: 9 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

-
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: 56.0 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: 1.5 µm / Nominal magnification: 130000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 137044
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER

+
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