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- PDB-4xp6: X-ray structure of Drosophila dopamine transporter bound to psych... -

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Basic information

Entry
Database: PDB / ID: 4xp6
TitleX-ray structure of Drosophila dopamine transporter bound to psychostimulant methamphetamine
Components
  • (Antibody fragment ...) x 2
  • Transporter
Keywordstranport protein/inhibitor / integral membrane protein / all-alpha helical antidepressant complex / tranport protein-inhibitor complex
Function / homology
Function and homology information


Dopamine clearance from the synaptic cleft / Na+/Cl- dependent neurotransmitter transporters / circadian sleep/wake cycle / response to odorant / cocaine binding / dopamine:sodium symporter activity / norepinephrine transport / regulation of presynaptic cytosolic calcium ion concentration / dopamine transport / symporter activity ...Dopamine clearance from the synaptic cleft / Na+/Cl- dependent neurotransmitter transporters / circadian sleep/wake cycle / response to odorant / cocaine binding / dopamine:sodium symporter activity / norepinephrine transport / regulation of presynaptic cytosolic calcium ion concentration / dopamine transport / symporter activity / sleep / neuronal cell body membrane / dopamine uptake involved in synaptic transmission / amino acid transport / 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
alpha-maltose / (2S)-N-methyl-1-phenylpropan-2-amine / CHOLESTEROL / CHOLESTEROL HEMISUCCINATE / Transporter / Sodium-dependent dopamine transporter
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsAravind, P. / 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 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 3, 2015Group: Database references
Revision 1.3Nov 22, 2017Group: Database references / Derived calculations ...Database references / Derived calculations / Refinement description / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / entity_src_nat / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _entity_src_nat.pdbx_alt_source_flag / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _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 / 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.type / _entity.formula_weight / _entity.pdbx_description / _entity.src_method / _entity.type / _struct_conn_type.id
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
Revision 2.2Oct 9, 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: Transporter
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)108,35711
Polymers106,6893
Non-polymers1,6688
Water39622
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)97.040, 141.370, 165.680
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Detailsbiological unit is the same as asym.

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Transporter


Mass: 59892.289 Da / Num. of mol.: 1
Mutation: V74A, L415A, deletion N(1-20), Deletion C(603-631), Deletion (162-202)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: DAT, Dmel_CG8380 / Cell line (production host): GnTI- / Production host: Homo sapiens (human) / References: UniProt: A0A0B4KEX2, UniProt: Q7K4Y6*PLUS

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Antibody , 2 types, 2 molecules LH

#2: Antibody Antibody fragment heavy chain-protein, 9D5-heavy chain


Mass: 23177.473 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#3: Antibody Antibody fragment light chain-protein, 9D5-light chain


Mass: 23619.430 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)

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Sugars , 2 types, 2 molecules

#4: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-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: alpha-maltose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#8: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 6 types, 28 molecules

#5: Chemical ChemComp-B40 / (2S)-N-methyl-1-phenylpropan-2-amine / Methamphetamine


Mass: 149.233 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N
#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
#9: Chemical ChemComp-CLR / CHOLESTEROL


Mass: 386.654 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H46O
#10: Chemical ChemComp-Y01 / CHOLESTEROL HEMISUCCINATE


Mass: 486.726 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C31H50O4
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 22 / 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: 5.33 Å3/Da / Density % sol: 76.91 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: PEG 400 (38%), Tris (0.1M) / PH range: pH 8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 19, 2014
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.1→45.45 Å / Num. obs: 41149 / % possible obs: 97.7 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 98.84 Å2 / Rmerge F obs: 0.998 / Rmerge(I) obs: 0.102 / Rrim(I) all: 0.111 / Χ2: 1.038 / Net I/σ(I): 10.14 / Num. measured all: 234177
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
3.1-3.180.381.60.914871306129881.78297.6
3.18-3.270.61.1071.416522299429671.2299.1
3.27-3.360.7140.8431.9117198293629120.92299.2
3.36-3.470.7950.6292.6116197281227670.68998.4
3.47-3.580.8840.4523.5615820272627030.49599.2
3.58-3.710.9330.4184.4214136267025430.4695.2
3.71-3.850.960.2785.7714805259225470.30598.3
3.85-40.9750.1997.914059246724220.21898.2
4-4.180.9860.14510.1913791238623510.15898.5
4.18-4.380.9910.10513.4213038226822260.11598.1
4.38-4.620.9940.0915.7512456217621370.09898.2
4.62-4.90.9940.08316.8611804206720280.0998.1
4.9-5.240.9950.07617.4910899192518850.08497.9
5.24-5.660.9960.07118.0810263182317830.07797.8
5.66-6.20.9950.0718.239302167416250.07797.1
6.2-6.930.9960.06320.058342152814790.06996.8
6.93-80.9960.05123.227297135713180.05697.1
8-9.80.9980.04126.416202116411190.04596.1
9.8-13.860.9980.03927.3448209288830.04395.2
13.860.9980.03526.8223555444660.03985.7

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XSCALEdata scaling
PDB_EXTRACT3.15data extraction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4M48

4m48


Resolution: 3.1→45.45 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2588 2066 5.03 %
Rwork0.2357 --
obs0.2368 41113 97.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.1→45.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7441 0 114 22 7577
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0027791
X-RAY DIFFRACTIONf_angle_d0.59910645
X-RAY DIFFRACTIONf_dihedral_angle_d10.5242656
X-RAY DIFFRACTIONf_chiral_restr0.0421202
X-RAY DIFFRACTIONf_plane_restr0.0031315
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1-3.17210.35771420.35242553X-RAY DIFFRACTION97
3.1721-3.25140.35961310.31532616X-RAY DIFFRACTION99
3.2514-3.33930.31751400.30782577X-RAY DIFFRACTION99
3.3393-3.43750.34861340.28922608X-RAY DIFFRACTION99
3.4375-3.54850.30351460.28582581X-RAY DIFFRACTION99
3.5485-3.67520.341410.34172516X-RAY DIFFRACTION96
3.6752-3.82230.33381410.28142578X-RAY DIFFRACTION98
3.8223-3.99620.2881270.24882601X-RAY DIFFRACTION98
3.9962-4.20670.27311160.21742637X-RAY DIFFRACTION98
4.2067-4.47010.18671360.19542598X-RAY DIFFRACTION98
4.4701-4.81480.24331420.19182618X-RAY DIFFRACTION98
4.8148-5.29870.23291450.20462625X-RAY DIFFRACTION98
5.2987-6.06390.24791610.22722592X-RAY DIFFRACTION97
6.0639-7.6340.23541300.22642648X-RAY DIFFRACTION97
7.634-45.45470.22331340.21712699X-RAY DIFFRACTION94

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