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- PDB-5mju: Structure of the thermostabilized EAAT1 cryst mutant in complex w... -

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Basic information

Entry
Database: PDB / ID: 5mju
TitleStructure of the thermostabilized EAAT1 cryst mutant in complex with the competititve inhibitor TFB-TBOA and the allosteric inhibitor UCPH101
ComponentsExcitatory amino acid transporter 1,Neutral amino acid transporter B(0),Excitatory amino acid transporter 1
KeywordsTRANSPORT PROTEIN / excitatory aminoacid transporter 1 / human glutamate transporter / TFB-TBOA / UCPH-101
Function / homology
Function and homology information


Defective SLC1A3 causes episodic ataxia 6 (EA6) / Astrocytic Glutamate-Glutamine Uptake And Metabolism / membrane protein complex / auditory behavior / neurotransmitter uptake / cranial nerve development / cell morphogenesis involved in neuron differentiation / glutamine secretion / gamma-aminobutyric acid biosynthetic process / high-affinity L-glutamate transmembrane transporter activity ...Defective SLC1A3 causes episodic ataxia 6 (EA6) / Astrocytic Glutamate-Glutamine Uptake And Metabolism / membrane protein complex / auditory behavior / neurotransmitter uptake / cranial nerve development / cell morphogenesis involved in neuron differentiation / glutamine secretion / gamma-aminobutyric acid biosynthetic process / high-affinity L-glutamate transmembrane transporter activity / glutamate:sodium symporter activity / L-glutamine import across plasma membrane / L-glutamate import / L-glutamine transmembrane transporter activity / glutamine transport / L-serine transmembrane transporter activity / Transport of inorganic cations/anions and amino acids/oligopeptides / ligand-gated channel activity / L-glutamate transmembrane transport / L-glutamate transmembrane transporter activity / D-aspartate import across plasma membrane / neutral amino acid transport / amino acid transmembrane transporter activity / L-aspartate transmembrane transporter activity / L-aspartate import across plasma membrane / Glutamate Neurotransmitter Release Cycle / Amino acid transport across the plasma membrane / neutral L-amino acid transmembrane transporter activity / L-glutamate import across plasma membrane / transepithelial transport / symporter activity / intracellular sodium ion homeostasis / cellular response to cocaine / neurotransmitter transport / antiporter activity / glutamate binding / amino acid transport / RHOJ GTPase cycle / RHOQ GTPase cycle / protein homotrimerization / neuromuscular process controlling balance / RHOH GTPase cycle / transport across blood-brain barrier / response to light stimulus / RAC3 GTPase cycle / positive regulation of synaptic transmission / monoatomic ion transport / chloride transmembrane transport / potassium ion transmembrane transport / RAC1 GTPase cycle / basal plasma membrane / erythrocyte differentiation / sensory perception of sound / response to wounding / melanosome / signaling receptor activity / virus receptor activity / cytoplasmic vesicle / chemical synaptic transmission / neuron projection / response to xenobiotic stimulus / response to antibiotic / neuronal cell body / synapse / perinuclear region of cytoplasm / cell surface / extracellular exosome / membrane / metal ion binding / plasma membrane
Similarity search - Function
Proton glutamate symport protein / Sodium:dicarboxylate symporter / : / Sodium:dicarboxylate symporter family signature 2. / Sodium:dicarboxylate symporter / Sodium:dicarboxylate symporter, conserved site / Sodium:dicarboxylate symporter superfamily / Sodium:dicarboxylate symporter family / Sodium:dicarboxylate symporter family signature 1. / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-6Z6 / Chem-7O9 / Excitatory amino acid transporter 1 / Neutral amino acid transporter B(0)
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.71 Å
AuthorsCanul-Tec, J. / Assal, R. / Legrand, P. / Reyes, N.
Funding support France, 1items
OrganizationGrant numberCountry
ERC Starting Grant309657 France
CitationJournal: Nature / Year: 2017
Title: Structure and allosteric inhibition of excitatory amino acid transporter 1.
Authors: Canul-Tec, J.C. / Assal, R. / Cirri, E. / Legrand, P. / Brier, S. / Chamot-Rooke, J. / Reyes, N.
History
DepositionDec 1, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 19, 2017Provider: repository / Type: Initial release
Revision 1.1May 3, 2017Group: Database references
Revision 1.2May 10, 2017Group: Database references
Revision 1.3Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Excitatory amino acid transporter 1,Neutral amino acid transporter B(0),Excitatory amino acid transporter 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,3613
Polymers56,5121
Non-polymers8492
Water00
1
A: Excitatory amino acid transporter 1,Neutral amino acid transporter B(0),Excitatory amino acid transporter 1
hetero molecules

A: Excitatory amino acid transporter 1,Neutral amino acid transporter B(0),Excitatory amino acid transporter 1
hetero molecules

A: Excitatory amino acid transporter 1,Neutral amino acid transporter B(0),Excitatory amino acid transporter 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)172,0849
Polymers169,5373
Non-polymers2,5466
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_875-y+3,x-y+2,z1
crystal symmetry operation3_685-x+y+1,-x+3,z1
Buried area7700 Å2
ΔGint-68 kcal/mol
Surface area48830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.330, 124.330, 90.810
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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Components

#1: Protein Excitatory amino acid transporter 1,Neutral amino acid transporter B(0),Excitatory amino acid transporter 1 / Sodium-dependent glutamate/aspartate transporter 1 / GLAST-1 / Solute carrier family 1 member 3 / ...Sodium-dependent glutamate/aspartate transporter 1 / GLAST-1 / Solute carrier family 1 member 3 / ATB(0) / Baboon M7 virus receptor / RD114/simian type D retrovirus receptor / Sodium-dependent neutral amino acid transporter type 2 / Solute carrier family 1 member 5 / Sodium-dependent glutamate/aspartate transporter 1 / GLAST-1 / Solute carrier family 1 member 3


Mass: 56512.379 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: SLC1A3, EAAT1, GLAST, GLAST1, SLC1A5, ASCT2, M7V1, RDR, RDRC
Plasmid: pcDNA3 / Cell (production host): Epithelial / Cell line (production host): HEK-293F / Organ (production host): Kidney / Production host: Homo sapiens (human) / Tissue (production host): Embryonic kidney / References: UniProt: P43003, UniProt: Q15758
#2: Chemical ChemComp-6Z6 / 2-Amino-5,6,7,8-tetrahydro-4-(4-methoxyphenyl)-7-(naphthalen-1-yl)-5-oxo-4H-chromene-3-carbonitrile


Mass: 422.475 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H22N2O3
#3: Chemical ChemComp-7O9 / (2~{S},3~{S})-2-azanyl-3-[[3-[[4-(trifluoromethyl)phenyl]carbonylamino]phenyl]methoxy]butanedioic acid


Mass: 426.343 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H17F3N2O6

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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: 3.59 Å3/Da / Density % sol: 64.8 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.2
Details: 32% PEG 400, 100 mM Tris pH 8.2, 50 mM Calcium chloride, 50 mM Barium chloride
PH range: 8.0 - 8.4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9772 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 28, 2016
RadiationMonochromator: channel cut monocromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9772 Å / Relative weight: 1
ReflectionResolution: 3.71→46.31 Å / Num. obs: 8570 / % possible obs: 99.9 % / Redundancy: 16.6 % / Biso Wilson estimate: 109.76 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.14 / Rsym value: 0.051 / Net I/σ(I): 12.1
Reflection shellResolution: 3.71→3.81 Å / Redundancy: 17.7 % / Rmerge(I) obs: 3.7 / Mean I/σ(I) obs: 0.9 / CC1/2: 0.373 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSBUILT=20160617data reduction
XSCALEBUILT=20160617data scaling
PHASER2.5.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5LLM

5llm


Resolution: 3.71→25 Å / Cor.coef. Fo:Fc: 0.8455 / Cor.coef. Fo:Fc free: 0.7923 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.65
RfactorNum. reflection% reflectionSelection details
Rfree0.2543 684 9.97 %RANDOM
Rwork0.2268 ---
obs0.2297 6860 80.26 %-
Displacement parametersBiso mean: 135.41 Å2
Baniso -1Baniso -2Baniso -3
1-10.1728 Å20 Å20 Å2
2--10.1728 Å20 Å2
3----20.3455 Å2
Refine analyzeLuzzati coordinate error obs: 0.561 Å
Refinement stepCycle: 1 / Resolution: 3.71→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3008 0 62 0 3070
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0093119HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.034240HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1068SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes49HARMONIC2
X-RAY DIFFRACTIONt_gen_planes494HARMONIC5
X-RAY DIFFRACTIONt_it3119HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion1.77
X-RAY DIFFRACTIONt_other_torsion22.24
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion433SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3908SEMIHARMONIC4
LS refinement shellResolution: 3.71→4.15 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.2254 89 9.05 %
Rwork0.1918 894 -
all0.1953 983 -
obs--40.49 %
Refinement TLS params.Method: refined / Origin x: 53.9697 Å / Origin y: 155.7897 Å / Origin z: 1.539 Å
111213212223313233
T0.3407 Å2-0.1283 Å20.0846 Å2--0.0598 Å20.0343 Å2---0.6079 Å2
L0.0864 °2-0.0499 °20.0201 °2--0.0864 °20.369 °2--0.5428 °2
S-0.1161 Å °0.0284 Å °0.182 Å °-0.0231 Å °-0.2326 Å °-0.0091 Å °0.5897 Å °0.0432 Å °0.3487 Å °
Refinement TLS groupSelection details: { A|* }

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