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- PDB-4xp9: X-ray structure of Drosophila dopamine transporter bound to psych... -

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Basic information

Entry
Database: PDB / ID: 4xp9
TitleX-ray structure of Drosophila dopamine transporter bound to psychostimulant D-amphetamine
Components
  • (ANTIBODY FRAGMENT ...) x 2
  • TransporterTransport protein
Keywordstransport protein/inhibitor / integral membrane protein / all-alpha helical antidepressant complex / membrane protein / protein transport / transport protein-inhibitor complex
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 / dopamine:sodium symporter activity / norepinephrine:sodium symporter activity / norepinephrine transport / regulation of presynaptic cytosolic calcium ion concentration / dopamine transport ...Dopamine clearance from the synaptic cleft / Na+/Cl- dependent neurotransmitter transporters / circadian sleep/wake cycle / response to odorant / cocaine binding / dopamine:sodium symporter activity / norepinephrine:sodium symporter activity / norepinephrine transport / regulation of presynaptic cytosolic calcium ion concentration / dopamine transport / symporter activity / sleep / amino acid transport / dopamine uptake involved in synaptic transmission / neuronal cell body membrane / sodium ion transmembrane transport / adult locomotory behavior / presynaptic membrane / axon / membrane / 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
alpha-maltose / (2S)-1-phenylpropan-2-amine / CHOLESTEROL / 1-ETHOXY-2-(2-ETHOXYETHOXY)ETHANE / CHOLESTEROL HEMISUCCINATE / Transporter / Sodium-dependent dopamine transporter
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsAravind, P. / Wang, K. / 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 1.1May 27, 2015Group: Database references
Revision 1.2Jun 3, 2015Group: Database references
Revision 1.3Nov 25, 2015Group: Other
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_oper_list / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.pdbx_formal_charge / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.type / _pdbx_struct_oper_list.symmetry_operation / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Transporter
L: ANTIBODY FRAGMENT HEAVY CHAIN-PROTEIN, 9D5-HEAVY CHAIN
H: ANTIBODY FRAGMENT LIGHT CHAIN-PROTEIN, 9D5-LIGHT CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,72614
Polymers107,5393
Non-polymers2,18711
Water59433
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7120 Å2
ΔGint-40 kcal/mol
Surface area39170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.348, 140.748, 166.760
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules C

#1: Protein Transporter / Transport protein


Mass: 60728.301 Da / Num. of mol.: 1 / Mutation: V74A, L415A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: DAT, CG8380, Dmel_CG8380 / Cell line (production host): GnTI-HEK293s / Production host: Homo sapiens (human) / References: UniProt: A0A0B4KEX2, UniProt: Q7K4Y6*PLUS

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Antibody , 2 types, 2 molecules LH

#2: Antibody ANTIBODY FRAGMENT HEAVY CHAIN-PROTEIN, 9D5-HEAVY CHAIN


Mass: 23191.498 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse)
#3: Antibody ANTIBODY FRAGMENT LIGHT CHAIN-PROTEIN, 9D5-LIGHT CHAIN


Mass: 23619.430 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse)

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Sugars , 2 types, 2 molecules

#4: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#6: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 8 types, 42 molecules

#5: Chemical ChemComp-Y01 / CHOLESTEROL HEMISUCCINATE


Mass: 486.726 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C31H50O4
#7: Chemical ChemComp-MPO / 3[N-MORPHOLINO]PROPANE SULFONIC ACID / MOPS


Mass: 209.263 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H15NO4S / Comment: pH buffer*YM
#8: Chemical ChemComp-CLR / CHOLESTEROL / Cholesterol


Mass: 386.654 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H46O
#9: Chemical ChemComp-1WE / (2S)-1-phenylpropan-2-amine / Dextroamphetamine / D-amphetamine / Dexamphetamine / Dexedrine / Dextrostat / Dextroamphetamine


Mass: 135.206 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H13N
#10: Chemical ChemComp-P4G / 1-ETHOXY-2-(2-ETHOXYETHOXY)ETHANE / Diethylene glycol diethyl ether


Mass: 162.227 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O3
#11: Chemical ChemComp-NA / SODIUM ION


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


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#13: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 33 / Source method: isolated from a natural source / Formula: H2O

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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: 5.33 Å3/Da / Density % sol: 76.94 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: PEG 600 (36%), MOPS (0.1M)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 19, 2014
RadiationMonochromator: Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 55464 / % possible obs: 96.6 % / Redundancy: 3.7 % / Net I/σ(I): 18.1

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Processing

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

4m48


Resolution: 2.8→46.72 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 0.04 / Phase error: 26.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.242 5175 4.88 %
Rwork0.211 --
obs0.212 55464 96.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 85.19 Å2
Refinement stepCycle: LAST / Resolution: 2.8→46.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7484 0 148 33 7665
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0077859
X-RAY DIFFRACTIONf_angle_d1.16810723
X-RAY DIFFRACTIONf_dihedral_angle_d13.2082695
X-RAY DIFFRACTIONf_chiral_restr0.0441207
X-RAY DIFFRACTIONf_plane_restr0.0061321
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7952-2.82690.43741140.40022112X-RAY DIFFRACTION62
2.8269-2.86020.35081460.38072938X-RAY DIFFRACTION84
2.8602-2.8950.37911520.34083262X-RAY DIFFRACTION94
2.895-2.93170.37341870.34453179X-RAY DIFFRACTION93
2.9317-2.97030.32111600.31563244X-RAY DIFFRACTION93
2.9703-3.01090.32931660.30923243X-RAY DIFFRACTION94
3.0109-3.05390.27131480.30443449X-RAY DIFFRACTION97
3.0539-3.09950.30141470.28713390X-RAY DIFFRACTION98
3.0995-3.14790.31712020.28623436X-RAY DIFFRACTION98
3.1479-3.19950.30891790.27053408X-RAY DIFFRACTION99
3.1995-3.25470.32811570.27223492X-RAY DIFFRACTION100
3.2547-3.31390.29691830.26273483X-RAY DIFFRACTION100
3.3139-3.37760.29251710.24933438X-RAY DIFFRACTION100
3.3776-3.44650.24541730.24423492X-RAY DIFFRACTION100
3.4465-3.52140.25661890.23633482X-RAY DIFFRACTION100
3.5214-3.60330.26431670.23393454X-RAY DIFFRACTION100
3.6033-3.69340.2731820.23243464X-RAY DIFFRACTION100
3.6934-3.79320.25811780.22453465X-RAY DIFFRACTION99
3.7932-3.90480.24232230.20783416X-RAY DIFFRACTION100
3.9048-4.03070.26011620.2043461X-RAY DIFFRACTION100
4.0307-4.17470.23911540.1873493X-RAY DIFFRACTION100
4.1747-4.34180.20341630.17873460X-RAY DIFFRACTION100
4.3418-4.53920.20131920.17313460X-RAY DIFFRACTION100
4.5392-4.77830.22791630.17113470X-RAY DIFFRACTION100
4.7783-5.07730.21771800.17923488X-RAY DIFFRACTION100
5.0773-5.46880.23161890.19063440X-RAY DIFFRACTION100
5.4688-6.01810.24261760.20153474X-RAY DIFFRACTION100
6.0181-6.88660.22232070.20273430X-RAY DIFFRACTION100
6.8866-8.66730.18791640.16013464X-RAY DIFFRACTION99
8.6673-46.73090.21152010.20223318X-RAY DIFFRACTION96

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