[English] 日本語
Yorodumi
- EMDB-65401: Cryo-EM structure of human serotonin transporter in complex with ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-65401
TitleCryo-EM structure of human serotonin transporter in complex with tesofensine
Map data
Sample
  • Complex: Cryo-EM structure of human serotonin transporter in complex with tesofensine
    • Protein or peptide: Sodium-dependent serotonin transporter
  • Ligand: CHLORIDE ION
  • Ligand: SODIUM ION
  • Ligand: (1~{R},2~{R},3~{S},5~{S})-3-(3,4-dichlorophenyl)-2-(ethoxymethyl)-8-methyl-8-azabicyclo[3.2.1]octane
  • Ligand: CHOLESTEROL HEMISUCCINATE
KeywordsCryo-EM structure of human serotonin transporter in complex with tesofensine / MEMBRANE PROTEIN
Function / homology
Function and homology information


negative regulation of cerebellar granule cell precursor proliferation / regulation of thalamus size / Serotonin clearance from the synaptic cleft / serotonergic synapse / positive regulation of serotonin secretion / cocaine binding / negative regulation of organ growth / negative regulation of synaptic transmission, dopaminergic / serotonin:sodium:chloride symporter activity / cellular response to cGMP ...negative regulation of cerebellar granule cell precursor proliferation / regulation of thalamus size / Serotonin clearance from the synaptic cleft / serotonergic synapse / positive regulation of serotonin secretion / cocaine binding / negative regulation of organ growth / negative regulation of synaptic transmission, dopaminergic / serotonin:sodium:chloride symporter activity / cellular response to cGMP / sodium ion binding / enteric nervous system development / serotonin uptake / neurotransmitter transmembrane transporter activity / vasoconstriction / brain morphogenesis / monoamine transmembrane transporter activity / : / serotonin binding / antiporter activity / negative regulation of neuron differentiation / syntaxin-1 binding / male mating behavior / nitric-oxide synthase binding / neurotransmitter transport / amino acid transport / membrane depolarization / conditioned place preference / cellular response to retinoic acid / monoatomic cation channel activity / behavioral response to cocaine / response to nutrient / positive regulation of cell cycle / endomembrane system / sodium ion transmembrane transport / circadian rhythm / memory / platelet aggregation / integrin binding / response to toxic substance / actin filament binding / response to estradiol / presynaptic membrane / response to hypoxia / postsynaptic membrane / endosome membrane / neuron projection / response to xenobiotic stimulus / membrane raft / focal adhesion / positive regulation of gene expression / synapse / identical protein binding / plasma membrane
Similarity search - Function
Sodium:neurotransmitter symporter, serotonin, N-terminal / Serotonin (5-HT) neurotransmitter transporter, N-terminus / 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-dependent serotonin transporter
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsZhao Y / Li Y / Meng Y
Funding support China, 1 items
OrganizationGrant numberCountry
Chinese Academy of Sciences China
CitationJournal: To Be Published
Title: Cryo-EM structure of human serotonin transporter in complex with tesofensine
Authors: Zhao Y / Li Y / Meng Y
History
DepositionJul 17, 2025-
Header (metadata) releaseJul 22, 2026-
Map releaseJul 22, 2026-
UpdateJul 22, 2026-
Current statusJul 22, 2026Processing site: PDBc / Status: Released

-
Structure visualization

Supplemental images

emd_65401.png

Downloads & links

-
Map

FileDownload / File: emd_65401.map.gz / Format: CCP4 / Size: 64 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 256 pix.
= 217.6 Å		0.85 Å/pix.
x 256 pix.
= 217.6 Å		0.85 Å/pix.
x 256 pix.
= 217.6 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-1.410662 - 2.0213525
Average (Standard dev.)0.00042125676 (±0.0487422)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 217.6 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #2

Fileemd_65401_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_65401_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Cryo-EM structure of human serotonin transporter in complex with ...

EntireName: Cryo-EM structure of human serotonin transporter in complex with tesofensine
Components
  • Complex: Cryo-EM structure of human serotonin transporter in complex with tesofensine
    • Protein or peptide: Sodium-dependent serotonin transporter
  • Ligand: CHLORIDE ION
  • Ligand: SODIUM ION
  • Ligand: (1~{R},2~{R},3~{S},5~{S})-3-(3,4-dichlorophenyl)-2-(ethoxymethyl)-8-methyl-8-azabicyclo[3.2.1]octane
  • Ligand: CHOLESTEROL HEMISUCCINATE

-
Supramolecule #1: Cryo-EM structure of human serotonin transporter in complex with ...

SupramoleculeName: Cryo-EM structure of human serotonin transporter in complex with tesofensine
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

-
Macromolecule #1: Sodium-dependent serotonin transporter

MacromoleculeName: Sodium-dependent serotonin transporter / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 70.371305 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: METTPLNSQK QLSACEDGED CQENGVLQKV VPTPGDKVES GQISNGYSAV PSPGAGDDTR HSIPATTTTL VAELHQGERE TWGKKVDFL LSVIGYAVDL GNVWRFPYIC YQNGGGAFLL PYTIMAIFGG IPLFYMELAL GQYHRNGCIS IWRKICPIFK G IGYAICII ...String:
METTPLNSQK QLSACEDGED CQENGVLQKV VPTPGDKVES GQISNGYSAV PSPGAGDDTR HSIPATTTTL VAELHQGERE TWGKKVDFL LSVIGYAVDL GNVWRFPYIC YQNGGGAFLL PYTIMAIFGG IPLFYMELAL GQYHRNGCIS IWRKICPIFK G IGYAICII AFYIASYYNT IMAWALYYLI SSFTDQLPWT SCKNSWNTGN CTNYFSEDNI TWTLHSTSPA EEFYTRHVLQ IH RSKGLQD LGGISWQLAL CIMLIFTVIY FSIWKGVKTS GKVVWVTATF PYIILSVLLV RGATLPGAWR GVLFYLKPNW QKL LETGVW IDAAAQIFFS LGPGFGVLLA FASYNKFNNN CYQDALVTSV VNCMTSFVSG FVIFTVLGYM AEMRNEDVSE VAKD AGPSL LFITYAEAIA NMPASTFFAI IFFLMLITLG LDSTFAGLEG VITAVLDEFP HVWAKRRERF VLAVVITCFF GSLVT LTFG GAYVVKLLEE YATGPAVLTV ALIEAVAVSW FYGITQFCRD VKEMLGFSPG WFWRICWVAI SPLFLLFIIC SFLMSP PQL RLFQYNYPYW SIILGYCIGT SSFICIPTYI AYRLIITPGT FKERIIKSIT PETPTEIPCG DIRLNAV

UniProtKB: Sodium-dependent serotonin 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: SODIUM ION

MacromoleculeName: SODIUM ION / type: ligand / ID: 3 / Number of copies: 2
Molecular weightTheoretical: 22.99 Da

-
Macromolecule #4: (1~{R},2~{R},3~{S},5~{S})-3-(3,4-dichlorophenyl)-2-(ethoxymethyl)...

MacromoleculeName: (1~{R},2~{R},3~{S},5~{S})-3-(3,4-dichlorophenyl)-2-(ethoxymethyl)-8-methyl-8-azabicyclo[3.2.1]octane
type: ligand / ID: 4 / Number of copies: 1 / Formula: A1EA1
Molecular weightTheoretical: 328.277 Da

-
Macromolecule #5: CHOLESTEROL HEMISUCCINATE

MacromoleculeName: CHOLESTEROL HEMISUCCINATE / type: ligand / ID: 5 / Number of copies: 1 / Formula: Y01
Molecular weightTheoretical: 486.726 Da
Chemical component information

ChemComp-Y01:
CHOLESTEROL HEMISUCCINATE

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeTFS KRIOS
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
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: PHASE FLIPPING ONLY
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7lia

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 174344
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