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- PDB-4xpg: X-ray structure of Drosophila dopamine transporter with subsiteB ... -

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Basic information

Entry
Database: PDB / ID: 4xpg
TitleX-ray structure of Drosophila dopamine transporter with subsiteB mutations (D121G/S426M) bound to beta-CFT or Win35428
Components
  • (antibody fragment ...) x 2
  • Dopamine transporter
Keywordstransport protein/inhibitor / all alpha-helical integral membrane protein / transport protein-inhibitor complex
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-42L / CHOLESTEROL / Sodium-dependent dopamine transporter
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.21 Å
Model detailsD.melanogaster DAT construct with mutations V74A, D121G, L415A, S426M, with N-terminal deletion 1- ...D.melanogaster DAT construct with mutations V74A, D121G, L415A, S426M, with N-terminal deletion 1-20, EL2 deletion between 164-206 and C-terminal thrombin insertion at residues 602-607. Molecule crystallized in complexed with antibody fragment-9D5 using hanging-drop vapour diffusion method.
AuthorsPenmatsa, A. / Wang, K.H. / Gouaux, E.
CitationJournal: Nature / Year: 2015
Title: Neurotransmitter and psychostimulant recognition by the dopamine transporter.
Authors: Wang, K.H. / Penmatsa, A. / Gouaux, E.
History
DepositionJan 16, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 6, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 19, 2015Group: Database references
Revision 1.2Nov 22, 2017Group: Database references / Derived calculations / Refinement description
Category: citation / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.3Sep 27, 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 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Dopamine transporter
L: antibody fragment light chain
H: antibody fragment heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,9059
Polymers112,7733
Non-polymers1,1326
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)97.110, 140.080, 167.440
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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Protein , 1 types, 1 molecules A

#1: Protein Dopamine transporter


Mass: 60925.605 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: dDAT / Plasmid: pEG BacMam / Cell line (production host): GnTI-HEK293s / Production host: Homo Sapiens (human) / References: UniProt: Q7K4Y6*PLUS

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Antibody , 2 types, 2 molecules LH

#2: Antibody antibody fragment light chain


Mass: 25840.607 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): hybridoma / Production host: Mus musculus (house mouse)
#3: Antibody antibody fragment heavy chain


Mass: 26006.443 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): hybridoma / Production host: Mus musculus (house mouse)

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Non-polymers , 4 types, 6 molecules

#4: Chemical ChemComp-42L / methyl (1R,2S,3S,5S)-3-(4-fluorophenyl)-8-methyl-8-azabicyclo[3.2.1]octane-2-carboxylate


Mass: 277.334 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H20FNO2
#5: Chemical ChemComp-CLR / CHOLESTEROL


Mass: 386.654 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H46O
#6: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na

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Details

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: 5.36 Å3/Da / Density % sol: 77.05 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.8 / Details: PEG 400 38%, Bicine 0.1M

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 19, 2013
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.21→50 Å / Num. obs: 32879 / % possible obs: 86.7 % / Observed criterion σ(I): -3 / Redundancy: 4.8 % / Biso Wilson estimate: 87.24 Å2 / Rmerge F obs: 0.999 / Rmerge(I) obs: 0.081 / Rrim(I) all: 0.09 / Χ2: 0.966 / Net I/σ(I): 14.33 / Num. measured all: 156700
Reflection shellResolution: 3.21→3.3 Å / Rmerge F obs: 0.999 / Rmerge(I) obs: 0.73 / Mean I/σ(I) obs: 1.57 / Num. measured obs: 1723 / Num. possible: 499 / Num. unique obs: 395 / Rrim(I) all: 0.026 / Rejects: 0 / % possible all: 17.3

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Processing

Software
NameVersionClassification
PHENIXrefinement
XSCALEdata scaling
PDB_EXTRACT3.15data extraction
Cootmodel building
PHASERphasing
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4M48

4m48


Resolution: 3.21→48.39 Å / SU ML: 0.45 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.274 1669 5.08 %
Rwork0.251 31192 -
obs0.252 32861 86.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 151.85 Å2 / Biso mean: 80.03 Å2 / Biso min: 47.01 Å2
Refinement stepCycle: final / Resolution: 3.21→48.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7386 0 79 0 7465
Biso mean--76.71 --
Num. residues----961
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.2132-3.30780.3602350.361358762220
3.3078-3.41450.41421010.34381970207166
3.4145-3.53650.341540.32682743289794
3.5365-3.67810.43371610.40962794295594
3.6781-3.84540.34871720.32182792296495
3.8454-4.0480.29971340.28882912304696
4.048-4.30150.23811510.22532885303697
4.3015-4.63340.24721550.19912913306897
4.6334-5.09920.23221580.20142892305096
5.0992-5.8360.27241620.22542893305596
5.836-7.34860.23441300.23492917304795
7.3486-48.39580.22671560.22352894305091

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