[English] 日本語
Yorodumi
- EMDB-61562: membrane protein SLC6A3 with Bpp -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-61562
Titlemembrane protein SLC6A3 with Bpp
Map data
Sample
  • Complex: membrane protein
    • Protein or peptide: Sodium-dependent dopamine transporter
  • Ligand: Bupropion
  • Ligand: SODIUM ION
  • Ligand: water
Keywordsmembrane protein
Function / homology
Function and homology information


Defective neurotransmitter clearance by SLC6A3 causes Parkinsonism-dystonia infantile (PKDYS) / Defective transport of neurotransmitters by SLC6A3 causes Parkinsonism-dystonia infantile (PKDYS) / Dopamine clearance from the synaptic cleft / amine binding / dopamine uptake / adenohypophysis development / hyaloid vascular plexus regression / dopamine binding / norepinephrine:sodium symporter activity / dopamine:sodium symporter activity ...Defective neurotransmitter clearance by SLC6A3 causes Parkinsonism-dystonia infantile (PKDYS) / Defective transport of neurotransmitters by SLC6A3 causes Parkinsonism-dystonia infantile (PKDYS) / Dopamine clearance from the synaptic cleft / amine binding / dopamine uptake / adenohypophysis development / hyaloid vascular plexus regression / dopamine binding / norepinephrine:sodium symporter activity / dopamine:sodium symporter activity / neurotransmitter transmembrane transporter activity / regulation of dopamine metabolic process / flotillin complex / dopamine transport / dopamine catabolic process / dopaminergic synapse / monoamine transmembrane transporter activity / monoamine transport / positive regulation of multicellular organism growth / response to iron ion / heterocyclic compound binding / SLC-mediated transport of neurotransmitters / dopamine biosynthetic process / neurotransmitter transport / dopamine uptake involved in synaptic transmission / amino acid transport / prepulse inhibition / response to cAMP / lactation / axon terminus / protein phosphatase 2A binding / sodium ion transmembrane transport / response to nicotine / response to cocaine / locomotory behavior / cognition / sensory perception of smell / protease binding / presynaptic membrane / response to ethanol / postsynaptic membrane / neuron projection / membrane raft / response to xenobiotic stimulus / signaling receptor binding / axon / neuronal cell body / protein-containing complex binding / cell surface / membrane / metal ion binding / plasma membrane / cytoplasm
Similarity search - Function
Sodium:neurotransmitter symporter, dopamine / 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 dopamine transporter
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.69 Å
AuthorsZhang SS
Funding support China, 1 items
OrganizationGrant numberCountry
National Science Foundation (NSF, China)21532004 China
CitationJournal: To Be Published
Title: membrane transporter
Authors: Zhang SS
History
DepositionSep 16, 2024-
Header (metadata) releaseApr 8, 2026-
Map releaseApr 8, 2026-
UpdateApr 8, 2026-
Current statusApr 8, 2026Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_61562.png

Downloads & links

-
Map

FileDownload / File: emd_61562.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 240 pix.
= 202.392 Å		0.84 Å/pix.
x 240 pix.
= 202.392 Å		0.84 Å/pix.
x 240 pix.
= 202.392 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8433 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.331
Minimum - Maximum-2.2241871 - 3.6631944
Average (Standard dev.)-0.0019547741 (±0.075676404)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 202.392 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #1

Fileemd_61562_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_61562_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : membrane protein

EntireName: membrane protein
Components
  • Complex: membrane protein
    • Protein or peptide: Sodium-dependent dopamine transporter
  • Ligand: Bupropion
  • Ligand: SODIUM ION
  • Ligand: water

-
Supramolecule #1: membrane protein

SupramoleculeName: membrane protein / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

-
Macromolecule #1: Sodium-dependent dopamine transporter

MacromoleculeName: Sodium-dependent dopamine transporter / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 68.547469 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MSKSKCSVGL MSSVVAPAKE PNAVGPKEVE LILVKEQNGV QLTSSTLTNP RQSPVEAQDR ETWGKKIDFL LSVIGFAVDL ANVWRFPYL CYKNGGGAFL VPYLLFMVIA GMPLFYMELA LGQFNREGAA GVWKICPILK GVGFTVILIS LYVGFFYNVI I AWALHYLF ...String:
MSKSKCSVGL MSSVVAPAKE PNAVGPKEVE LILVKEQNGV QLTSSTLTNP RQSPVEAQDR ETWGKKIDFL LSVIGFAVDL ANVWRFPYL CYKNGGGAFL VPYLLFMVIA GMPLFYMELA LGQFNREGAA GVWKICPILK GVGFTVILIS LYVGFFYNVI I AWALHYLF SSFTTELPWI HCNNSWNSPN CSDAHPGDSS GDSSGLNDTF GTTPAAEYFE RGVLHLHQSH GIDDLGPPRW QL TACLVLV IVLLYFSLWK GVKTSGKVVW ITATMPYVVL TALLLRGVTL PGAIDGIRAY LSVDFYRLCE ASVWIDAATQ VCF SLGVGF GVLIAFSSYN KFTNNCYRDA IVTTSINSLT SFSSGFVVFS FLGYMAQKHS VPIGDVAKDG PGLIFIIYPE AIAT LPLSS AWAVVFFIML LTLGIDSAMG GMESVITGLI DEFQLLHRHR ELFTLFIVLA TFLLSLFCVT NGGIYVFTLL DHFAA GTSI LFGVLIEAIG VAWFYGVGQF SDDIQQMTGQ RPSLYWRLCW KLVSPCFLLF VVVVSIVTFR PPHYGAYIFP DWANAL GWV IATSSMAMVP IYAAYKFCSL PGSFREKLAY AIAPEKDREL VDRGEVRQFT LRHWLKV

UniProtKB: Sodium-dependent dopamine transporter

-
Macromolecule #2: Bupropion

MacromoleculeName: Bupropion / type: ligand / ID: 2 / Number of copies: 1 / Formula: 1XR
Molecular weightTheoretical: 239.741 Da

-
Macromolecule #3: SODIUM ION

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

-
Macromolecule #4: water

MacromoleculeName: water / type: ligand / ID: 4 / Number of copies: 1 / 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: 7.2
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.69 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 253000
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

+
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