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- PDB-6m2r: X-ray structure of a functional Drosophila dopamine transporter i... -

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Basic information

Entry
Database: PDB / ID: 6m2r
TitleX-ray structure of a functional Drosophila dopamine transporter in L-norepinephrine bound form
Components
  • (Antibody fragment 9D5 ...) x 2
  • Sodium-dependent dopamine transporter
KeywordsMEMBRANE PROTEIN / neurotransmitter transporter / antibody fragment
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
CHOLESTEROL / DECANE / L-NOREPINEPHRINE / CHOLESTEROL HEMISUCCINATE / Sodium-dependent dopamine transporter
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.802 Å
AuthorsShabareesh, P. / Mallela, A.K. / Joseph, D. / Penmatsa, A.
Funding support India, 2items
OrganizationGrant numberCountry
Department of Biotechnology (DBT, India)IA/1/15/2/502063 India
Department of Biotechnology (DBT, India)BT/09/IYBA/2015/13 India
CitationJournal: Nat Commun / Year: 2021
Title: Structural basis of norepinephrine recognition and transport inhibition in neurotransmitter transporters.
Authors: Pidathala, S. / Mallela, A.K. / Joseph, D. / Penmatsa, A.
History
DepositionFeb 28, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 17, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 29, 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 1.3Oct 9, 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: Sodium-dependent dopamine transporter
L: Antibody fragment 9D5 Light chain
H: Antibody fragment 9D5 heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,12015
Polymers107,0413
Non-polymers2,07912
Water1,78399
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)96.800, 141.270, 167.711
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 9D5 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): Sf9 / Production host: Spodoptera frugiperda (fall armyworm)
#3: Antibody Antibody fragment 9D5 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): Sf9 / Production host: Spodoptera frugiperda (fall armyworm)

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein Sodium-dependent dopamine transporter / Protein fumin


Mass: 60114.523 Da / Num. of mol.: 1
Mutation: N-terminal deletion 24, V74A, Deletion 162-202, L415A, F471L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: DAT, fmn, CG8380 / Cell line (production host): HEK293 GnTI- / Production host: Homo sapiens (human) / References: UniProt: Q7K4Y6
#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 , 7 types, 110 molecules

#5: Chemical ChemComp-Y01 / CHOLESTEROL HEMISUCCINATE


Mass: 486.726 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C31H50O4
#6: Chemical ChemComp-CLR / CHOLESTEROL


Mass: 386.654 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H46O
#7: Chemical ChemComp-LNR / L-NOREPINEPHRINE / NORADRENALINE


Mass: 169.178 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H11NO3 / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#10: Chemical ChemComp-D10 / DECANE


Mass: 142.282 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H22
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 99 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 5.36 Å3/Da / Density % sol: 77.04 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.8 / Details: 32% PEG 600, 0.1M MOPS pH6.8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 12, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.8→48.41 Å / Num. obs: 57216 / % possible obs: 99.8 % / Redundancy: 6.2 % / Biso Wilson estimate: 71.35 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.095 / Rpim(I) all: 0.042 / Rrim(I) all: 0.104 / Net I/σ(I): 15.1 / Num. measured all: 352537 / Scaling rejects: 5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.8-2.885.81.2452517443400.6310.5611.3691.498.5
12.21-48.414.90.02537557650.9990.0130.02858.797.1

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Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
PHENIX1.13_2998refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4XP1

4xp1


Resolution: 2.802→48.4 Å / SU ML: 0.43 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.61
RfactorNum. reflection% reflection
Rfree0.2469 2785 4.88 %
Rwork0.2108 --
obs0.2126 57115 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 141.85 Å2 / Biso mean: 64.2973 Å2 / Biso min: 36.11 Å2
Refinement stepCycle: final / Resolution: 2.802→48.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7533 0 154 99 7786
Biso mean--79.34 60.07 -
Num. residues----969
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection Rwork% reflection obs (%)
2.802-2.85020.44011390.3602263898
2.8502-2.9020.33621270.31292680100
2.902-2.95780.32381300.28212717100
2.9578-3.01820.29621540.26742656100
3.0182-3.08380.33181460.27212661100
3.0838-3.15560.31611230.25032705100
3.1556-3.23440.31361170.24152747100
3.2344-3.32190.2841560.23892664100
3.3219-3.41960.27141790.23822645100
3.4196-3.52990.2761280.2262725100
3.5299-3.65610.24991270.21132705100
3.6561-3.80240.25181350.20442720100
3.8024-3.97540.25591140.20372708100
3.9754-4.18490.24481400.19572744100
4.1849-4.44690.1991420.1752704100
4.4469-4.78990.23091460.17092742100
4.7899-5.27150.22441260.16972734100
5.2715-6.0330.2321520.19332765100
6.033-7.59620.21231510.20182777100
7.5962-48.40.246915350.2108289399

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