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- PDB-4xpf: X-ray structure of Drosophila dopamine transporter with subsiteB ... -

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Basic information

Entry
Database: PDB / ID: 4xpf
TitleX-ray structure of Drosophila dopamine transporter with subsiteB mutations (D121G/S426M) bound to RTI-55
Components
  • (ANTIBODY FRAGMENT ...) x 2
  • Dopamine transporter-protein
Keywordstransport protein/inhibitor / all alpha-helical integral membrane protein / 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 / dopamine:sodium symporter activity / norepinephrine:sodium symporter activity / norepinephrine transport / response to odorant / regulation of presynaptic cytosolic calcium ion concentration / dopamine transport ...Dopamine clearance from the synaptic cleft / Na+/Cl- dependent neurotransmitter transporters / circadian sleep/wake cycle / cocaine binding / dopamine:sodium symporter activity / norepinephrine:sodium symporter activity / norepinephrine transport / response to odorant / regulation of presynaptic cytosolic calcium ion concentration / dopamine transport / sleep / dopamine uptake involved in synaptic transmission / amino acid transport / 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
Chem-42F / CHOLESTEROL / 1-ETHOXY-2-(2-ETHOXYETHOXY)ETHANE / Sodium-dependent dopamine transporter
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.273 Å
Model detailsD.melanogaster DAT construct with mutations V74A, D121G, L415A, S426M, with N-terminal deletion 1- ...D.melanogaster DAT construct with mutations V74A, D121G, L415A, S426M, with N-terminal deletion 1-20, EL2 deletion between 164-206 and C-terminal thrombin insertion at residues 602-607. Molecule crystallized in complexed with antibody fragment-9D5 using hanging-drop vapour diffusion method.
AuthorsPenmatsa, A. / Wang, K.H. / Gouaux, E.
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 1.1Aug 19, 2015Group: Database references
Revision 1.2Aug 26, 2015Group: Structure summary
Revision 1.3Sep 27, 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_oper_list / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_conn.ptnr2_label_seq_id / _struct_conn_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Dopamine transporter-protein
L: ANTIBODY FRAGMENT HEAVY CHAIN-PROTEIN, 9D5-HEAVY CHAIN
H: ANTIBODY FRAGMENT LIGHT CHAIN-PROTEIN, 9D5-LIGHT CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,57211
Polymers112,6883
Non-polymers1,8858
Water1086
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)97.415, 140.312, 166.962
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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Antibody , 2 types, 2 molecules LH

#2: Antibody ANTIBODY FRAGMENT HEAVY CHAIN-PROTEIN, 9D5-HEAVY CHAIN


Mass: 25840.607 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Description: hybridoma cells / Cell line (production host): hybridoma / Production host: Mus musculus (house mouse)
#3: Antibody ANTIBODY FRAGMENT LIGHT CHAIN-PROTEIN, 9D5-LIGHT CHAIN


Mass: 25921.338 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Description: hybridoma cells / Cell line (production host): hybridoma / Production host: Mus musculus (house mouse)

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein Dopamine transporter-protein


Mass: 60925.605 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: dDAT / Plasmid: pEG BacMam / Cell line (production host): GnTI-, HEK293s / Production host: Homo sapiens (human) / References: UniProt: Q7K4Y6*PLUS
#4: Sugar ChemComp-DMU / DECYL-BETA-D-MALTOPYRANOSIDE / DECYLMALTOSIDE


Type: D-saccharide / Mass: 482.562 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C22H42O11 / Comment: detergent*YM

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Non-polymers , 6 types, 13 molecules

#5: Chemical ChemComp-P4G / 1-ETHOXY-2-(2-ETHOXYETHOXY)ETHANE


Mass: 162.227 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O3
#6: 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
#7: Chemical ChemComp-CLR / CHOLESTEROL


Mass: 386.654 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H46O
#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
#10: 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: 5.37 Å3/Da / Density % sol: 77.11 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 8.8 / Details: PEG 400 39%, Bicine 0.1M

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.24 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 24, 2013
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.24 Å / Relative weight: 1
ReflectionResolution: 3.27→50 Å / Num. obs: 32190 / % possible obs: 89.4 % / Redundancy: 3.9 % / Biso Wilson estimate: 114.2 Å2 / Rmerge(I) obs: 0.12 / Χ2: 3.345 / Net I/av σ(I): 18.721 / Net I/σ(I): 9 / Num. measured all: 126634
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Num. unique allΧ2% possible allRmerge(I) obs
3.27-3.393.432152.68691.3
3.39-3.523.832702.92792.3
3.52-3.683.832563.21291.80.838
3.68-3.883.832802.99691.50.743
3.88-4.123.932293.093910.432
4.12-4.44432533.23990.90.218
4.44-4.884.132203.45689.70.147
4.88-5.594.232013.45688.50.121
5.59-7.044.331683.56386.70.106
7.04-50430984.657810.06

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Processing

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

4m48


Resolution: 3.273→48.324 Å / SU ML: 0.6 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 36.19 / Stereochemistry target values: ML
Details: Residue H CYS 134 and Residue H GLY 139 are not properly linked: distance between C and N is 10.88.
RfactorNum. reflection% reflection
Rfree0.2962 1605 5.01 %
Rwork0.2412 30434 -
obs0.2439 32039 89.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 307.85 Å2 / Biso mean: 110.3196 Å2 / Biso min: 20 Å2
Refinement stepCycle: final / Resolution: 3.273→48.324 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7385 0 141 6 7532
Biso mean--124.13 99.41 -
Num. residues----961
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0057735
X-RAY DIFFRACTIONf_angle_d0.9210559
X-RAY DIFFRACTIONf_chiral_restr0.0371188
X-RAY DIFFRACTIONf_plane_restr0.0041301
X-RAY DIFFRACTIONf_dihedral_angle_d13.9072686
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.2733-3.37890.44221360.40772728286489
3.3789-3.49970.43631750.39292772294792
3.4997-3.63970.40091510.35262819297092
3.6397-3.80530.38721410.35782774291591
3.8053-4.00580.35451470.30792795294291
4.0058-4.25670.33091440.23392810295491
4.2567-4.58510.24991520.18852788294091
4.5851-5.04610.25411310.18092800293189
5.0461-5.77520.24541430.19962754289788
5.7752-7.27220.26931290.23342742287186
7.2722-48.32890.27051560.21482652280881

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