[English] 日本語
Yorodumi
- PDB-6m0f: X-ray structure of Drosophila dopamine transporter with subsiteB ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6m0f
TitleX-ray structure of Drosophila dopamine transporter with subsiteB mutations (D121G/S426M) in substrate-free form
Components
  • (Antibody fragment (9D5) ...) x 2
  • Sodium-dependent dopamine transporter
KeywordsMEMBRANE PROTEIN / neurotransmitter transporter / antibody fragment
Function / homology
Function and homology information


Dopamine clearance from the synaptic cleft / Na+/Cl- dependent neurotransmitter transporters / dopamine:sodium symporter activity / norepinephrine transport / circadian sleep/wake cycle / response to odorant / cocaine binding / regulation of presynaptic cytosolic calcium ion concentration / dopamine transport / sleep ...Dopamine clearance from the synaptic cleft / Na+/Cl- dependent neurotransmitter transporters / dopamine:sodium symporter activity / norepinephrine transport / circadian sleep/wake cycle / response to odorant / cocaine binding / regulation of presynaptic cytosolic calcium ion concentration / dopamine transport / sleep / dopamine uptake involved in synaptic transmission / neuronal cell body membrane / sodium ion transmembrane transport / adult locomotory behavior / presynaptic membrane / neuron projection / metal ion binding / plasma membrane
Similarity search - Function
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
CHOLESTEROL / 1-ETHOXY-2-(2-ETHOXYETHOXY)ETHANE / Sodium-dependent dopamine transporter
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsShabareesh, P. / Mallela, A.K. / Joseph, D. / Penmatsa, A.
Funding support India, 2items
OrganizationGrant numberCountry
Department of Biotechnology (DBT, India)IA/1/15/2/502063 India
Department of Biotechnology (DBT, India)BT/09/IYBA/2015/13 India
CitationJournal: Nat Commun / Year: 2021
Title: Structural basis of norepinephrine recognition and transport inhibition in neurotransmitter transporters.
Authors: Pidathala, S. / Mallela, A.K. / Joseph, D. / Penmatsa, A.
History
DepositionFeb 21, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 17, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Sodium-dependent dopamine transporter
L: Antibody fragment (9D5) Light chain
H: Antibody fragment (9D5) heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,8219
Polymers106,8043
Non-polymers1,0176
Water1448
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, monomeric transporter in complex with antibody fragment
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)97.978, 133.472, 162.088
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein Sodium-dependent dopamine transporter / Protein fumin


Mass: 59878.367 Da / Num. of mol.: 1
Mutation: Deletion of N-terminal 1-24 and 162-202, V74A, D121G, L415A, S426M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: DAT, fmn, CG8380 / Cell line (production host): HEK293 GnTI- / Production host: Homo sapiens (human) / References: UniProt: Q7K4Y6

-
Antibody , 2 types, 2 molecules LH

#2: Antibody Antibody fragment (9D5) Light chain


Mass: 23306.586 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm)
#3: Antibody Antibody fragment (9D5) heavy chain


Mass: 23619.430 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm)

-
Non-polymers , 5 types, 14 molecules

#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-CLR / CHOLESTEROL / Cholesterol


Mass: 386.654 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H46O
#6: Chemical ChemComp-P4G / 1-ETHOXY-2-(2-ETHOXYETHOXY)ETHANE / Diethylene glycol diethyl ether


Mass: 162.227 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O3 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 4.96 Å3/Da / Density % sol: 75.21 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.1M MOPS, pH 7.0, 30% PEG 600

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.968 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 3, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.968 Å / Relative weight: 1
ReflectionResolution: 3.299→48.99 Å / Num. obs: 32667 / % possible obs: 99.7 % / Redundancy: 5.5 % / Biso Wilson estimate: 118.12 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.117 / Rpim(I) all: 0.054 / Rrim(I) all: 0.129 / Net I/σ(I): 9.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
3.3-3.485.41.5572484846440.5530.7371.729198.8
10.43-48.994.90.036557811300.9990.0180.0433.497.5

-
Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
Aimlessdata scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4XNX

4xnx


Resolution: 3.3→48.989 Å / SU ML: 0.52 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 32.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2773 1629 5 %Random
Rwork0.2414 30929 --
obs0.2433 32558 99.54 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 175.07 Å2 / Biso mean: 112.9067 Å2 / Biso min: 74.66 Å2
Refinement stepCycle: final / Resolution: 3.3→48.989 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7430 0 70 8 7508
Biso mean--117.02 92.34 -
Num. residues----967
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.3-3.39590.41991480.3783247097
3.3959-3.50550.37641250.34372574100
3.5055-3.63070.39931350.31442534100
3.6307-3.7760.32571180.27452548100
3.776-3.94780.31531310.27372566100
3.9478-4.15580.28331240.25142560100
4.1558-4.41610.23431270.22172575100
4.4161-4.75680.23741330.19792570100
4.7568-5.2350.24631640.19992564100
5.235-5.99130.2661500.22152590100
5.9913-7.5440.26891390.23932648100
7.544-48.9890.27141350.2411273099

+
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