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- PDB-4m48: X-ray structure of dopamine transporter elucidates antidepressant... -

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Basic information

Entry
Database: PDB / ID: 4m48
TitleX-ray structure of dopamine transporter elucidates antidepressant mechanism
Components
  • (9D5 antibody, ...) x 2
  • Transporter
KeywordsTRANSPORT PROTEIN / SLC6 / neurotransmitter transporter
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 / dopamine:sodium symporter activity / regulation of presynaptic cytosolic calcium ion concentration / norepinephrine transport / dopamine transport / sleep ...Dopamine clearance from the synaptic cleft / Na+/Cl- dependent neurotransmitter transporters / circadian sleep/wake cycle / cocaine binding / response to odorant / dopamine:sodium symporter activity / regulation of presynaptic cytosolic calcium ion concentration / norepinephrine transport / dopamine transport / sleep / amino acid transport / dopamine uptake involved in synaptic transmission / neuronal cell body membrane / 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
Nortriptyline / CHOLESTEROL / Sodium-dependent dopamine transporter / Sodium-dependent dopamine transporter
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.955 Å
AuthorsGouaux, E. / Penmatsa, A. / Wang, K.
CitationJournal: Nature / Year: 2013
Title: X-ray structure of dopamine transporter elucidates antidepressant mechanism.
Authors: Penmatsa, A. / Wang, K.H. / Gouaux, E.
History
DepositionAug 6, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 18, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 2, 2013Group: Database references
Revision 1.2Oct 9, 2013Group: Derived calculations
Revision 1.3Nov 13, 2013Group: Database references
Revision 1.4Jul 26, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.5Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transporter
L: 9D5 antibody, light chain
H: 9D5 antibody, heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,4338
Polymers112,7013
Non-polymers7315
Water57632
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)97.839, 133.684, 162.443
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 A

#1: Protein Transporter / dopamine transporter / GFP


Mass: 60939.520 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999
Mutation: V74A V275A V311A L415A G538L, delta 1-20, delta 164-206, delta 603-631
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: DAT, CG8380 / Cell line (production host): HEK / Production host: Homo sapiens (human) / References: UniProt: Q9NB97, UniProt: Q7K4Y6*PLUS

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Antibody , 2 types, 2 molecules LH

#2: Antibody 9D5 antibody, light chain


Mass: 25840.607 Da / Num. of mol.: 1 / Fragment: Fab, papain cleavage fragment / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#3: Antibody 9D5 antibody, heavy chain


Mass: 25921.338 Da / Num. of mol.: 1 / Fragment: Fab, papain cleavage fragment / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)

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Non-polymers , 5 types, 37 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-21B / Nortriptyline / 3-(10,11-dihydro-5H-dibenzo[a,d][7]annulen-5-ylidene)-N-methylpropan-1-amine


Mass: 263.377 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H21N / Comment: antidepressant*YM
#7: Chemical ChemComp-CLR / CHOLESTEROL


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


Mass: 18.015 Da / Num. of mol.: 32 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Sequence detailsCHAIN A COMPRISES RESIDUES 21-163 AND 207-601 OF DOPAMINE TRANSPORTER (UNP Q9NB97).

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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: 4.71 Å3/Da / Density % sol: 73.9 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 100 mM glycine, pH 9.0, 38% PEG350 MME, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 15, 2013
RadiationMonochromator: Cryo-Cooled double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.955→103.224 Å / Num. all: 45350 / Num. obs: 42168 / % possible obs: 93.3 % / Observed criterion σ(I): 1.35 / Redundancy: 4.7 % / Biso Wilson estimate: 90 Å2 / Rmerge(I) obs: 0.098 / Net I/σ(I): 10.9
Reflection shellResolution: 2.955→3.07 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.955 / Mean I/σ(I) obs: 1.05 / % possible all: 94.7

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: dev_1402)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3F3A

3f3a


Resolution: 2.955→47.376 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.7898 / SU ML: 0.51 / σ(F): 1.35 / Phase error: 27.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2564 2084 4.94 %
Rwork0.221 40061 -
obs0.2226 42145 92.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 140.83 Å2 / Biso mean: 83.3568 Å2 / Biso min: 54.01 Å2
Refinement stepCycle: LAST / Resolution: 2.955→47.376 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7405 0 51 32 7488
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0047690
X-RAY DIFFRACTIONf_angle_d0.82410491
X-RAY DIFFRACTIONf_chiral_restr0.0541166
X-RAY DIFFRACTIONf_plane_restr0.0041305
X-RAY DIFFRACTIONf_dihedral_angle_d11.5892625
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.955-3.02350.41861150.36262548266390
3.0235-3.09910.36641450.34062686283195
3.0991-3.18280.36741560.3072675283195
3.1828-3.27650.29631470.27662663281094
3.2765-3.38220.30741250.25072710283594
3.3822-3.50310.27131560.22822661281794
3.5031-3.64330.2911430.22552667281094
3.6433-3.8090.25681360.21312673280994
3.809-4.00970.21271350.19772680281593
4.0097-4.26080.24391240.18452681280593
4.2608-4.58950.22691300.1832694282493
4.5895-5.05090.18131310.17412664279592
5.0509-5.78070.24831500.19382659280992
5.7807-7.27880.24911450.2232668281391
7.2788-47.38220.27081460.24522732287889

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