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- PDB-7wlw: X-ray structure of thermostabilized Drosophila dopamine transport... -

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Basic information

Entry
Database: PDB / ID: 7wlw
TitleX-ray structure of thermostabilized Drosophila dopamine transporter with GABA transporter1-like substitutions in the binding site, in complex with SKF89976a
Components
  • Antibody Fragment heavy chain
  • Antibody fragment light chain
  • Sodium-dependent dopamine transporter
KeywordsMEMBRANE PROTEIN / neurotransmitter transporter
Function / homology
Function and homology information


Dopamine clearance from the synaptic cleft / SLC-mediated transport of neurotransmitters / 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 / SLC-mediated transport of neurotransmitters / 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-1WR / 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: 2.9 Å
AuthorsPenmatsa, A. / Joseph, D.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Biotechnology (DBT, India)IA/I/15/2/502063 India
CitationJournal: Embo J. / Year: 2022
Title: Structural insights into GABA transport inhibition using an engineered neurotransmitter transporter.
Authors: Joseph, D. / Nayak, S.R. / Penmatsa, A.
History
DepositionJan 13, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 29, 2022Provider: repository / Type: Initial release
Revision 1.1Jul 20, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Aug 17, 2022Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Oct 23, 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 light chain
H: Antibody Fragment heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,17911
Polymers107,0713
Non-polymers2,1088
Water70339
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)96.780, 141.755, 168.236
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 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 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: 60144.594 Da / Num. of mol.: 1
Mutation: V74A,V275A,L415A,V311A, G538L; F43Y, D46G, V120L, D121N, S422Q, G425T, S426V, A117S, F325L, V327S, E384S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: DAT, fmn, CG8380 / Cell line (production host): HEK293S / 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: obtained synthetically / Formula: C22H42O11 / Comment: detergent*YM

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Non-polymers , 6 types, 46 molecules

#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-1WR / (3S)-1-(4,4-diphenylbut-3-enyl)piperidine-3-carboxylic acid / SKF89976A


Mass: 335.439 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H25NO2 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-Y01 / CHOLESTEROL HEMISUCCINATE


Mass: 486.726 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C31H50O4
#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.: 39 / 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: 5.39 Å3/Da / Density % sol: 77.18 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 36% PEG 600, 0.1M MOPS pH6.5, 0.5mM SKF89976A / PH range: 6.2-6.8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 21, 2021
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.9→47.29 Å / Num. obs: 51978 / % possible obs: 99.8 % / Redundancy: 5.4 % / Biso Wilson estimate: 74.81 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.139 / Rpim(I) all: 0.066 / Rrim(I) all: 0.154 / Net I/σ(I): 11.3 / Num. measured all: 278702 / Scaling rejects: 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
2.9-2.995.31.6562345543900.4430.7821.835198.5
11.96-47.294.40.02235828140.9990.0120.02650.596.3

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Processing

Software
NameVersionClassification
PHENIX1.20rc4_4425refinement
XDSdata reduction
Aimless0.7.3data scaling
PDB_EXTRACT3.27data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4XNX

4xnx


Resolution: 2.9→39.96 Å / SU ML: 0.43 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 28.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2639 2521 4.87 %
Rwork0.235 49206 -
obs0.2365 51727 99.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 145.16 Å2 / Biso mean: 68.5165 Å2 / Biso min: 36.16 Å2
Refinement stepCycle: final / Resolution: 2.9→39.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7535 0 147 39 7721
Biso mean--84.45 62.05 -
Num. residues----971
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 18

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.9-2.960.39511380.33732634277297
2.96-3.020.35871440.313927282872100
3.02-3.080.42411070.354227272834100
3.08-3.150.36481470.313226922839100
3.15-3.230.34321500.287927142864100
3.23-3.320.34241360.261326942830100
3.32-3.420.28791320.251427182850100
3.42-3.530.29261380.25527432881100
3.53-3.650.27641380.28842649278797
3.65-3.80.39271430.36952654279798
3.8-3.970.30261250.226327432868100
3.97-4.180.23641290.206527622891100
4.18-4.440.20551350.184727652900100
4.44-4.790.19271450.181327402885100
4.79-5.270.17771480.18327452893100
5.27-6.030.24511440.206727882932100
6.03-7.580.22751470.224728152962100
7.58-39.960.26621750.21922895307099

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