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

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Basic information

Entry
Database: PDB / ID: 4xph
TitleX-ray structure of Drosophila dopamine transporter with subsiteB mutations (D121G/S426M) bound to 3,4dichlorophenethylamine
Components
  • (Antibody fragment ...) x 2
  • Transporter
Keywordsprotein transport/inhibitor / integral membrane protein / neurotransmitter transporter / protein transport-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
beta-maltose / 2-(3,4-dichlorophenyl)ethanamine / CHOLESTEROL / 1-ETHOXY-2-(2-ETHOXYETHOXY)ETHANE / Sodium-dependent dopamine transporter / Sodium-dependent dopamine transporter
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.9 Å
AuthorsPenmatsa, A. / Wang, K. / 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 17, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 6, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 19, 2015Group: Database references
Revision 1.2Nov 22, 2017Group: Database references / Derived calculations / Refinement description
Category: citation / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _pdbx_struct_oper_list.symmetry_operation / _software.classification
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 / pdbx_struct_conn_angle / struct_asym / 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_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_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.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _struct_asym.entity_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 30, 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: Transporter
L: Antibody fragment light chain
H: Antibody fragment heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,39112
Polymers106,8183
Non-polymers1,5729
Water27015
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)97.968, 144.665, 165.666
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 light chain


Mass: 23320.611 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: 23619.430 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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Protein / Sugars , 2 types, 2 molecules A

#1: Protein Transporter


Mass: 59878.367 Da / Num. of mol.: 1
Mutation: V74A, L415A, D121G, S426M, DEL 162-202, DEL1-20, DEL603-631
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: DAT, CG8380 / Cell line (production host): HEK293s / Production host: Homo sapiens (human) / References: UniProt: Q9NB97, 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 , 6 types, 23 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-42J / 2-(3,4-dichlorophenyl)ethanamine


Mass: 190.070 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H9Cl2N
#7: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#8: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 386.654 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H46O
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 15 / 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: 5.5 Å3/Da / Density % sol: 77.62 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 6.5 / Details: PEG 400, 33%; NaMES

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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 8, 2014
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 52939 / % possible obs: 97.2 % / Redundancy: 3.8 % / Biso Wilson estimate: 92.33 Å2 / Rmerge(I) obs: 0.074 / Χ2: 2.187 / Net I/av σ(I): 23.667 / Net I/σ(I): 12.4 / Num. measured all: 203265
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Num. unique allΧ2% possible allRmerge(I) obs
2.9-33.953501.33899.8
3-3.123.953561.44999.6
3.12-3.273.953631.7199.70.695
3.27-3.443.953371.92399.60.466
3.44-3.653.853852.38299.50.317
3.65-3.943.143682.91880.60.185
3.94-4.333.951442.47694.40.092
4.33-4.964.154602.71999.90.064
4.96-6.24454992.82799.90.06
6.24-503.856772.38498.70.036

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Processing

Software
NameVersionClassification
PHENIXrefinement
SCALEPACKdata scaling
PDB_EXTRACT3.15data extraction
HKL-2000data scaling
PHASERphasing
RefinementResolution: 2.9→48.106 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 32.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.277 2673 5.08 %
Rwork0.2403 49959 -
obs0.2422 52632 95.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 169.75 Å2 / Biso mean: 92.0325 Å2 / Biso min: 60.57 Å2
Refinement stepCycle: final / Resolution: 2.9→48.106 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7480 0 105 15 7600
Biso mean--106.96 86.21 -
Num. residues----967
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0047815
X-RAY DIFFRACTIONf_angle_d0.89410660
X-RAY DIFFRACTIONf_chiral_restr0.0351193
X-RAY DIFFRACTIONf_plane_restr0.0041317
X-RAY DIFFRACTIONf_dihedral_angle_d12.5662689
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 19

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.8566-2.90850.388990.34441857195668
2.9085-2.96440.33841420.34042730287299
2.9644-3.02490.36951340.33432693282799
3.0249-3.09070.37411320.326127342866100
3.0907-3.16260.33971490.319927292878100
3.1626-3.24160.36471480.31527022850100
3.2416-3.32930.28691530.30212710286399
3.3293-3.42720.33091410.29682743288499
3.4272-3.53780.35891500.293227052855100
3.5378-3.66420.32971470.34932326247386
3.6642-3.81080.40431090.34452134224378
3.8108-3.98420.35431250.30952300242584
3.9842-4.19410.26941390.224327692908100
4.1941-4.45680.21411600.192927492909100
4.4568-4.80060.221500.188127602910100
4.8006-5.28310.2481530.191627782931100
5.2831-6.04630.22951250.210828322957100
6.0463-7.61290.26491560.218428342990100
7.6129-48.11280.25981610.21262874303597

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