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

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Basic information

Entry
Database: PDB / ID: 4xnu
TitleX-ray structure of Drosophila dopamine transporter in complex with nisoxetine
Components
  • (antibody fragment ...) x 2
  • Integral membrane protein-dopamine transporter
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 / 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
nisoxetine / CHOLESTEROL / Sodium-dependent dopamine transporter
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.98 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 1.4Sep 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 1.5Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Integral membrane protein-dopamine transporter
L: antibody fragment light chain
H: antibody fragment heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,6518
Polymers108,9123
Non-polymers7395
Water1448
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)96.901, 133.667, 161.682
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 Integral membrane protein-dopamine transporter


Mass: 59684.055 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Cell line (production host): HEK293-GnTI / 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: 23306.586 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: 25921.338 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 , 5 types, 13 molecules

#4: Chemical ChemComp-NA / SODIUM ION


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


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-CLR / CHOLESTEROL


Mass: 386.654 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H46O
#7: Chemical ChemComp-41U / nisoxetine / (3S)-3-(2-methoxyphenoxy)-N-methyl-3-phenylpropan-1-amine


Mass: 271.354 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21NO2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: H2O

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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: 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: 2.98→50 Å / Num. obs: 44010 / % possible obs: 99.4 % / Redundancy: 5.1 % / Biso Wilson estimate: 92.53 Å2 / Rmerge(I) obs: 0.133 / Rpim(I) all: 0.069 / Rrim(I) all: 0.137 / Χ2: 0.629 / Net I/av σ(I): 12.857 / Net I/σ(I): 3.9 / Num. measured all: 223836
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Num. unique allCC1/2Rpim(I) allΧ2% possible allRmerge(I) obsRrim(I) all
2.98-3.093.843140.4730.7050.4499.1
3.09-3.214.543180.6290.6320.44399.4
3.21-3.364.743540.7290.4580.46399.60.915
3.36-3.535.543790.6440.330.52499.90.720.794
3.53-3.755.543910.9350.2150.56999.80.4720.52
3.75-4.045.343930.9620.1460.59699.80.3160.349
4.04-4.455.443970.9860.0770.67499.60.1670.184
4.45-5.095.544010.9910.0540.72599.70.1180.131
5.09-6.425.444750.9930.0460.6199.50.0980.108
6.42-505.245880.9950.0251.10597.80.0530.059

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Processing

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

4m48


Resolution: 2.98→47.099 Å / FOM work R set: 0.7844 / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 27.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2514 1971 4.55 %
Rwork0.2259 41380 -
obs0.227 43351 98.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 177.48 Å2 / Biso mean: 85.68 Å2 / Biso min: 43.24 Å2
Refinement stepCycle: final / Resolution: 2.98→47.099 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7395 0 51 8 7454
Biso mean--96.83 93.05 -
Num. residues----962
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0047688
X-RAY DIFFRACTIONf_angle_d0.84610491
X-RAY DIFFRACTIONf_chiral_restr0.0381168
X-RAY DIFFRACTIONf_plane_restr0.0041306
X-RAY DIFFRACTIONf_dihedral_angle_d11.7232619
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.9716-3.04590.31061170.28132434255182
3.0459-3.12820.34631410.286829623103100
3.1282-3.22020.29231390.274129273066100
3.2202-3.32410.35641410.258429693110100
3.3241-3.44290.28721420.236729753117100
3.4429-3.58070.26981400.233729423082100
3.5807-3.74360.24781430.231529883131100
3.7436-3.94090.25961420.22729743116100
3.9409-4.18770.22521410.218729793120100
4.1877-4.51070.25971420.19529853127100
4.5107-4.96420.2121440.190630183162100
4.9642-5.68150.22131440.209530293173100
5.6815-7.15410.2621460.239230503196100
7.1541-47.10530.24341490.23473148329798

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