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- PDB-4xnx: X-ray structure of Drosophila dopamine transporter in complex wit... -

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Basic information

Entry
Database: PDB / ID: 4xnx
TitleX-ray structure of Drosophila dopamine transporter in complex with reboxetine
Components
  • Antibody fragment heavy chain
  • Transporter
  • antibody fragment light chain
Keywordstransport protein/inhibitor / integral membrane protein / all-alpha helical antidepressant complex / 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 / cocaine binding / response to odorant / regulation of presynaptic cytosolic calcium ion concentration / dopamine:sodium symporter activity / norepinephrine transport / dopamine transport / symporter activity ...Dopamine clearance from the synaptic cleft / Na+/Cl- dependent neurotransmitter transporters / circadian sleep/wake cycle / cocaine binding / response to odorant / regulation of presynaptic cytosolic calcium ion concentration / dopamine:sodium symporter activity / norepinephrine transport / 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
beta-maltose / Chem-41X / CHOLESTEROL / Transporter / Sodium-dependent dopamine transporter
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsAravind, P. / Wang, K. / Gouaux, E.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2015
Title: X-ray structures of Drosophila dopamine transporter in complex with nisoxetine and reboxetine.
Authors: Penmatsa, A. / Wang, K.H. / Gouaux, E.
History
DepositionJan 16, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 13, 2015Provider: repository / Type: Initial release
Revision 1.1May 27, 2015Group: Database references
Revision 1.2Jun 10, 2015Group: Database references
Revision 1.3May 31, 2017Group: 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 / 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 / _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
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
A: Transporter
L: antibody fragment light chain
H: Antibody fragment heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,88710
Polymers109,3763
Non-polymers1,5107
Water1086
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)97.673, 141.036, 167.247
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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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: 25921.338 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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Protein / Sugars , 2 types, 2 molecules A

#1: Protein Transporter


Mass: 60148.539 Da / Num. of mol.: 1 / Mutation: V74, L415A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: DAT, Dmel_CG8380 / Cell line (production host): GnTI-HEK293s / Production host: Homo sapiens (human) / References: UniProt: A0A0B4KEX2, UniProt: Q7K4Y6*PLUS
#4: Polysaccharide alpha-D-glucopyranose-(1-4)-beta-D-glucopyranose / beta-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: beta-maltose
DescriptorTypeProgram
DGlcpa1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5][a2122h-1a_1-5]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][a-D-Glcp]{}}LINUCSPDB-CARE

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Non-polymers , 5 types, 12 molecules

#5: Chemical ChemComp-CLR / CHOLESTEROL


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


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


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#8: Chemical ChemComp-41X / (2R)-2-[(R)-(2-ethoxyphenoxy)(phenyl)methyl]morpholine / Reboxetine


Mass: 313.391 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H23NO3 / Comment: antidepressant, inhibitor*YM
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / 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: 4.92 Å3/Da / Density % sol: 75.02 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: PEG 350 MME 38%, Glycine 0.1M / PH range: 9

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.979 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Mar 15, 2013
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.997→48.417 Å / Num. obs: 46863 / % possible obs: 99.4 % / Redundancy: 14.4 % / Biso Wilson estimate: 116.6 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 5.6
Reflection shellResolution: 3→3.11 Å / Redundancy: 14 % / Rmerge(I) obs: 0.866 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIXrefinement
HKL-2000data reduction
PDB_EXTRACT3.15data extraction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4M48

4m48


Resolution: 3→48.42 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.6 / Stereochemistry target values: ML
Details: Residue H CYS 134 and Residue H THR 138 are not properly linked: distance between C and N is 9.24.
RfactorNum. reflection% reflection
Rfree0.258 1978 4.28 %
Rwork0.217 --
obs0.219 46217 98.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 110.3 Å2
Refinement stepCycle: LAST / Resolution: 3→48.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7401 0 105 6 7512
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0057737
X-RAY DIFFRACTIONf_angle_d0.90810583
X-RAY DIFFRACTIONf_dihedral_angle_d12.9572635
X-RAY DIFFRACTIONf_chiral_restr0.0371193
X-RAY DIFFRACTIONf_plane_restr0.0041307
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9972-3.07220.39091290.30832826X-RAY DIFFRACTION89
3.0722-3.15520.31091320.29662940X-RAY DIFFRACTION92
3.1552-3.24810.34311390.27653144X-RAY DIFFRACTION100
3.2481-3.35290.29681440.27453200X-RAY DIFFRACTION100
3.3529-3.47270.28771400.25273168X-RAY DIFFRACTION100
3.4727-3.61170.28521430.24163182X-RAY DIFFRACTION100
3.6117-3.7760.28461420.24953175X-RAY DIFFRACTION100
3.776-3.9750.24411430.23033208X-RAY DIFFRACTION100
3.975-4.22390.25621420.1983177X-RAY DIFFRACTION99
4.2239-4.54980.19641430.17423197X-RAY DIFFRACTION100
4.5498-5.00720.21031440.16983227X-RAY DIFFRACTION100
5.0072-5.73080.24641450.20263253X-RAY DIFFRACTION100
5.7308-7.21640.26711430.24073222X-RAY DIFFRACTION98
7.2164-48.42370.27311490.21763320X-RAY DIFFRACTION97

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