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- PDB-4xp1: X-ray structure of Drosophila dopamine transporter bound to neuro... -

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Basic information

Entry
Database: PDB / ID: 4xp1
TitleX-ray structure of Drosophila dopamine transporter bound to neurotransmitter dopamine
Components
  • Antibody fragment light chain
  • Dopamine transporter, isoform B
  • antibody fragment heavy chain
Keywordsmembrane protein/transport protein / integral membrane protein / membrane protein-transport protein complex
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 / symporter activity ...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 / symporter activity / sleep / dopamine uptake involved in synaptic transmission / neuronal cell body membrane / sodium ion transmembrane transport / adult locomotory behavior / presynaptic membrane / neuron projection / 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 / CHOLESTEROL / L-DOPAMINE / 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 / Resolution: 2.89 Å
AuthorsGouaux, E. / Penmatsa, A. / Wang, K.
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 22, 2017Group: Database references / Derived calculations ...Database references / Derived calculations / Refinement description / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Refinement 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_conn_angle / refine_hist / struct_asym / 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.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.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _refine_hist.d_res_high / _struct_asym.entity_id / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Dopamine transporter, isoform B
L: Antibody fragment light chain
H: antibody fragment heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,20815
Polymers106,9463
Non-polymers2,26112
Water37821
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)96.797, 140.181, 166.195
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, isoform B /


Mass: 60020.414 Da / Num. of mol.: 1 / Mutation: V74A, V415A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: DAT, Dmel_CG8380 / 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 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) / Production host: Mus musculus (house mouse)
#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) / Production host: Mus musculus (house mouse)

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Sugars , 2 types, 3 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.: 2
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
#7: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / 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, 30 molecules

#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#8: 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
#9: Chemical ChemComp-LDP / L-DOPAMINE / DOPAMINE / Dopamine (medication)


Mass: 153.178 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H11NO2 / Comment: medication*YM
#10: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#11: Chemical ChemComp-Y01 / CHOLESTEROL HEMISUCCINATE


Mass: 486.726 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C31H50O4
#12: Chemical ChemComp-CLR / CHOLESTEROL / Cholesterol


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


Mass: 18.015 Da / Num. of mol.: 21 / 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: 5.27 Å3/Da / Density % sol: 76.66 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: PEG 600 31%, Tris (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 315 / Detector: CCD / Date: Sep 21, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.89→44.983 Å / Num. obs: 94660 / % possible obs: 96.3 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 81.76 Å2 / Rmerge F obs: 0.998 / Rmerge(I) obs: 0.113 / Rrim(I) all: 0.129 / Χ2: 0.911 / Net I/σ(I): 11.35 / Num. measured all: 200565
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
2.89-3.060.361.6640.7324364820867061.93181.7
3.06-3.270.6560.8651.6831905768676560.9999.6
3.27-3.530.8610.4833.2529762717871420.55399.5
3.53-3.870.9460.2396.6627272665766160.27499.4
3.87-4.320.990.11312.3124739600659680.12999.4
4.32-4.990.9960.0620.4221907536053290.06999.4
4.99-6.090.9970.05321.7418534458545420.06199.1
6.09-8.540.9980.0428.6714113360135420.04698.4
8.540.9990.02346.387969216320430.02794.5

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Processing

Software
NameVersionClassification
PHENIXrefinement
Aimless0.2.17data scaling
PDB_EXTRACT3.15data extraction
SCALEPACKdata scaling
PHASERphasing
RefinementResolution: 2.89→44.983 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 0.11 / Phase error: 29.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2562 4646 4.91 %
Rwork0.2178 90014 -
obs0.2197 94660 96.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 157.96 Å2 / Biso mean: 75.2214 Å2 / Biso min: 20 Å2
Refinement stepCycle: final / Resolution: 2.89→44.983 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7472 0 182 21 7675
Biso mean--98.39 65.21 -
Num. residues----968
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0067858
X-RAY DIFFRACTIONf_angle_d1.05910723
X-RAY DIFFRACTIONf_chiral_restr0.0471209
X-RAY DIFFRACTIONf_plane_restr0.0051318
X-RAY DIFFRACTIONf_dihedral_angle_d14.2432699
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.8894-2.92220.4486710.39711757182856
2.9222-2.95660.43141290.37242479260880
2.9566-2.99260.34461210.36072712283387
2.9926-3.03050.36421590.3592939309895
3.0305-3.07030.42921890.3553008319799
3.0703-3.11240.39441760.34631333309100
3.1124-3.15680.39611460.329230803226100
3.1568-3.2040.38241540.312330823236100
3.204-3.2540.3591530.303831253278100
3.254-3.30730.35141740.297530833257100
3.3073-3.36430.29141550.291530803235100
3.3643-3.42550.30841790.293630883267100
3.4255-3.49140.29211730.265930873260100
3.4914-3.56260.28141790.263730763255100
3.5626-3.640.31311390.248130803219100
3.64-3.72470.3341420.24283112325499
3.7247-3.81780.26721710.23593064323599
3.8178-3.92090.33661530.21923091324499
3.9209-4.03620.25481550.214931343289100
4.0362-4.16640.22141550.189130863241100
4.1664-4.31520.2141670.17163023319099
4.3152-4.48790.22451530.170731293282100
4.4879-4.69190.20111610.162330783239100
4.6919-4.9390.20381730.156930803253100
4.939-5.2480.21491210.16943094321599
5.248-5.65250.1781750.175531243299100
5.6525-6.220.21951540.193075322999
6.22-7.1170.23571460.17983082322899
7.117-8.9550.21241680.16633029319798
8.955-44.98830.22871550.23343004315997

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