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- PDB-6m38: X-ray structure of a Drosophila dopamine transporter with subsite... -

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Basic information

Entry
Database: PDB / ID: 6m38
TitleX-ray structure of a Drosophila dopamine transporter with subsiteB mutations (D121G/S426M) in S-duloxetine bound 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 / circadian sleep/wake cycle / response to odorant / cocaine binding / norepinephrine transport / dopamine:sodium symporter activity / regulation of presynaptic cytosolic calcium ion concentration / dopamine transport / sleep ...Dopamine clearance from the synaptic cleft / Na+/Cl- dependent neurotransmitter transporters / circadian sleep/wake cycle / response to odorant / cocaine binding / norepinephrine transport / dopamine:sodium symporter activity / regulation of presynaptic cytosolic calcium ion concentration / dopamine transport / sleep / neuronal cell body membrane / dopamine uptake involved in synaptic transmission / amino acid transport / sodium ion transmembrane transport / adult locomotory behavior / presynaptic membrane / axon / 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. / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Chem-29E / CHOLESTEROL / CHOLESTEROL HEMISUCCINATE / Sodium-dependent dopamine transporter
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.001 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
DepositionMar 2, 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
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)108,53910
Polymers106,8043
Non-polymers1,7357
Water43224
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)97.288, 140.641, 167.818
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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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)

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Protein / Sugars , 2 types, 2 molecules A

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


Mass: 59878.367 Da / Num. of mol.: 1
Mutation: N-terminal deletion 1-24, V74A, D121G, Deletion 162-202, 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
#8: Sugar ChemComp-DMU / DECYL-BETA-D-MALTOPYRANOSIDE / DECYLMALTOSIDE


Type: D-saccharide / Mass: 482.562 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C22H42O11 / Comment: detergent*YM

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Non-polymers , 6 types, 30 molecules

#4: Chemical ChemComp-29E / (3S)-N-methyl-3-(naphthalen-1-yloxy)-3-(thiophen-2-yl)propan-1-amine / Duloxetine


Mass: 297.415 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H19NOS / Feature type: SUBJECT OF INVESTIGATION / Comment: medication, inhibitor*YM
#5: Chemical ChemComp-Y01 / CHOLESTEROL HEMISUCCINATE


Mass: 486.726 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C31H50O4
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#7: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 386.654 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H46O
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 24 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 5.37 Å3/Da / Density % sol: 77.12 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.1M MOPS pH 7.0, 30% PEG 600

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 0.9789 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 21, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 3→48.644 Å / Num. obs: 46777 / % possible obs: 99.8 % / Redundancy: 7.3 % / Biso Wilson estimate: 86.16 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.111 / Rpim(I) all: 0.044 / Rrim(I) all: 0.119 / Net I/σ(I): 12.5
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
3-3.117.31.3943250844630.6040.5471.51.698.7
11.62-48.646.20.03956479180.9980.0180.04335.198.9

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
Aimless0.7.1data scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4XNX

4xnx


Resolution: 3.001→48.64 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.91
RfactorNum. reflection% reflection
Rfree0.2439 2316 4.96 %
Rwork0.215 --
obs0.2165 46693 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 147.91 Å2 / Biso mean: 78.2486 Å2 / Biso min: 30 Å2
Refinement stepCycle: final / Resolution: 3.001→48.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7494 0 120 24 7638
Biso mean--88.08 69.86 -
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 (%)
3.001-3.06220.36551260.3414251698
3.0622-3.12870.32091230.30282590100
3.1287-3.20150.30961530.27522557100
3.2015-3.28150.29831150.26742609100
3.2815-3.37020.30031430.25882570100
3.3702-3.46940.29691400.25132572100
3.4694-3.58130.28471330.24552607100
3.5813-3.70930.27291410.22782569100
3.7093-3.85780.271250.2112599100
3.8578-4.03330.20541360.20532596100
4.0333-4.24580.231300.1942621100
4.2458-4.51160.25021590.17772598100
4.5116-4.85970.20051360.17082625100
4.8597-5.34820.22731280.18262634100
5.3482-6.12080.21121500.20712647100
6.1208-7.70660.23541510.20242661100
7.7066-48.640.22831270.2315280699

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