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- PDB-4xp5: X-ray structure of Drosophila dopamine transporter bound to cocai... -

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Basic information

Entry
Database: PDB / ID: 4xp5
TitleX-ray structure of Drosophila dopamine transporter bound to cocaine analogue-RTI55
Components
  • Antibody fragment heavy chain-protein, 9D5-heavy chain
  • Dopamine transporter, isoform B
  • Ighg protein
Keywordstransport protein/inhibitor / integral membrane protein / membrane protein-transport protein complex / transport protein-inhibitor complex
Function / homology
Function and homology information


catecholamine uptake / Dopamine clearance from the synaptic cleft / Na+/Cl- dependent neurotransmitter transporters / sodium:chloride symporter activity / circadian sleep/wake cycle / response to odorant / cocaine binding / norepinephrine transport / dopamine:sodium symporter activity / regulation of presynaptic cytosolic calcium ion concentration ...catecholamine uptake / Dopamine clearance from the synaptic cleft / Na+/Cl- dependent neurotransmitter transporters / sodium:chloride symporter activity / circadian sleep/wake cycle / response to odorant / cocaine binding / norepinephrine transport / dopamine:sodium symporter activity / regulation of presynaptic cytosolic calcium ion concentration / dopamine transport / monoamine transmembrane transporter activity / sleep / neurotransmitter transport / 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
alpha-maltose / Chem-42F / CHOLESTEROL / 1-ETHOXY-2-(2-ETHOXYETHOXY)ETHANE / Transporter / Sodium-dependent dopamine transporter
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.3 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 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Source and taxonomy / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / citation / entity / entity_name_com / entity_src_gen / entity_src_nat / 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_atom_id / _atom_site.label_comp_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _citation.journal_id_CSD / _entity.formula_weight / _entity.pdbx_description / _entity.type / _entity_src_gen.pdbx_alt_source_flag / _entity_src_nat.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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
A: Dopamine transporter, isoform B
L: Antibody fragment heavy chain-protein, 9D5-heavy chain
H: Ighg protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,43411
Polymers106,6893
Non-polymers1,7458
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)95.250, 137.980, 163.390
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Detailsbiological unit is the same as asym.

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Components

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Antibody , 2 types, 2 molecules LH

#2: Antibody Antibody fragment heavy chain-protein, 9D5-heavy chain


Mass: 23177.473 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): GnTI-HEK293s / Production host: Mus musculus (house mouse)
#3: Antibody Ighg protein


Mass: 23619.430 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein Dopamine transporter, isoform B


Mass: 59892.289 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, Dmel_CG8380 / Production host: Homo sapiens (human) / References: UniProt: A0A0B4KEX2, UniProt: Q7K4Y6*PLUS
#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

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Non-polymers , 5 types, 7 molecules

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


Mass: 385.240 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H20INO2
#6: Chemical ChemComp-CLR / CHOLESTEROL


Mass: 386.654 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H46O
#7: Chemical ChemComp-P4G / 1-ETHOXY-2-(2-ETHOXYETHOXY)ETHANE


Mass: 162.227 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O3
#8: Chemical ChemComp-NA / SODIUM ION


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


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl

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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: 5.03 Å3/Da / Density % sol: 75.56 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: PEG 400 (41%), Tris (0.1M) / PH range: pH 8.0

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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: Feb 22, 2014
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.3→50 Å / Num. obs: 28495 / % possible obs: 86.2 % / Redundancy: 4.3 % / Net I/σ(I): 11

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Processing

Software
NameVersionClassification
PHENIXrefinement
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementResolution: 3.3→47.28 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 29.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2859 1440 5.05 %
Rwork0.2448 27055 -
obs0.2469 28495 86.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 151.69 Å2 / Biso mean: 72.9476 Å2 / Biso min: 20 Å2
Refinement stepCycle: final / Resolution: 3.3→47.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7389 0 131 0 7520
Biso mean--82.52 --
Num. residues----966
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0027745
X-RAY DIFFRACTIONf_angle_d0.69710593
X-RAY DIFFRACTIONf_chiral_restr0.0251200
X-RAY DIFFRACTIONf_plane_restr0.0031306
X-RAY DIFFRACTIONf_dihedral_angle_d11.5352660
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.2999-3.41780.3151580.34975103332
3.4178-3.55460.30261420.33312775291789
3.5546-3.71630.35821510.3262896304793
3.7163-3.91220.34631690.30032856302593
3.9122-4.15720.27851640.24332892305693
4.1572-4.47790.25291330.20672943307693
4.4779-4.92810.27711560.21342924308093
4.9281-5.64020.25771610.22852903306492
5.6402-7.10220.30971600.23642910307091
7.1022-47.28480.25541460.22162981312789

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