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- PDB-5lm4: Structure of the thermostalilized EAAT1 cryst-II mutant in comple... -

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Basic information

Entry
Database: PDB / ID: 5lm4
TitleStructure of the thermostalilized EAAT1 cryst-II mutant in complex with L-ASP and the allosteric inhibitor UCPH101
ComponentsExcitatory amino acid transporter 1,Neutral amino acid transporter B(0),Excitatory amino acid transporter 1
KeywordsTRANSPORT PROTEIN / excitatory amino acid transporter 1 / human glutamate transporter / SLC1A3 / UCPH101
Function / homology
Function and homology information


Defective SLC1A3 causes episodic ataxia 6 (EA6) / auditory behavior / Astrocytic Glutamate-Glutamine Uptake And Metabolism / membrane protein complex / glutamine secretion / neurotransmitter uptake / L-glutamine import across plasma membrane / cranial nerve development / cell morphogenesis involved in neuron differentiation / glutamine transport ...Defective SLC1A3 causes episodic ataxia 6 (EA6) / auditory behavior / Astrocytic Glutamate-Glutamine Uptake And Metabolism / membrane protein complex / glutamine secretion / neurotransmitter uptake / L-glutamine import across plasma membrane / cranial nerve development / cell morphogenesis involved in neuron differentiation / glutamine transport / L-glutamine transmembrane transporter activity / L-serine transmembrane transporter activity / gamma-aminobutyric acid biosynthetic process / ligand-gated channel activity / high-affinity L-glutamate transmembrane transporter activity / glutamate:sodium symporter activity / L-glutamate import / Transport of inorganic cations/anions and amino acids/oligopeptides / neutral amino acid transport / L-glutamate transmembrane transport / L-glutamate transmembrane transporter activity / D-aspartate import across plasma membrane / amino acid transmembrane transporter activity / Amino acid transport across the plasma membrane / L-aspartate transmembrane transporter activity / L-aspartate import across plasma membrane / neutral L-amino acid transmembrane transporter activity / Glutamate Neurotransmitter Release Cycle / L-glutamate import across plasma membrane / symporter activity / intracellular sodium ion homeostasis / transepithelial transport / neurotransmitter transport / antiporter activity / amino acid transport / cellular response to cocaine / glutamate binding / RHOJ GTPase cycle / RHOQ GTPase cycle / protein homotrimerization / RHOH GTPase cycle / neuromuscular process controlling balance / transport across blood-brain barrier / response to light stimulus / RAC3 GTPase cycle / positive regulation of synaptic transmission / monoatomic ion transport / potassium ion transmembrane transport / chloride transmembrane transport / RAC1 GTPase cycle / erythrocyte differentiation / basal plasma membrane / sensory perception of sound / response to wounding / melanosome / virus receptor activity / signaling 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 / ASPARTIC ACID / 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: 3.1 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
DepositionJul 29, 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 10, 2024Group: 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

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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)57,0394
Polymers56,4601
Non-polymers5793
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)123.110, 123.110, 89.620
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: 56460.324 Da / Num. of mol.: 1
Fragment: UNP residues 1-149,UNP residues 158-230,UNP residues 243-542
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): embrionic / Cell line (production host): HEK-293F / Production host: Homo sapiens (human) / Tissue (production host): embrionic kidney / References: UniProt: P43003, UniProt: Q15758
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-ASP / ASPARTIC ACID / Aspartic acid


Type: L-peptide linking / Mass: 133.103 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H7NO4
#4: 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

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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: 3.5 Å3/Da / Density % sol: 64.6 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.2
Details: 28% 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: ID23-2 / Wavelength: 0.976 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 6, 2016
RadiationMonochromator: Si (111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 3.1→45.82 Å / Num. all: 290672 / Num. obs: 14115 / % possible obs: 99.9 % / Redundancy: 20.6 % / Biso Wilson estimate: 121.37 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 15.8
Reflection shellResolution: 3.1→3.68 Å / Redundancy: 21.2 % / Rmerge(I) obs: 6.71 / Mean I/σ(I) obs: 0.8 / CC1/2: 0.434 / % possible all: 99.9

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSVERSION May 1, 2016 BUILT=20160517data reduction
XSCALEVERSION May 1, 2016 BUILT=20160517data scaling
PHASER2.5.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2NWX

2nwx


Resolution: 3.1→45.8 Å / Cor.coef. Fo:Fc: 0.885 / Cor.coef. Fo:Fc free: 0.7792 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.444
RfactorNum. reflection% reflectionSelection details
Rfree0.2586 528 4.92 %RANDOM
Rwork0.2167 ---
obs0.2188 10725 75.85 %-
Displacement parametersBiso mean: 111.65 Å2
Baniso -1Baniso -2Baniso -3
1-4.8649 Å20 Å20 Å2
2--4.8649 Å20 Å2
3----9.7298 Å2
Refine analyzeLuzzati coordinate error obs: 0.43 Å
Refinement stepCycle: LAST / Resolution: 3.1→45.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2959 0 42 0 3001
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013037HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.124127HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1038SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes50HARMONIC2
X-RAY DIFFRACTIONt_gen_planes465HARMONIC5
X-RAY DIFFRACTIONt_it3037HARMONIC20
X-RAY DIFFRACTIONt_nbd3SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.14
X-RAY DIFFRACTIONt_other_torsion20.67
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion425SEMIHARMONIC5
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_contact3874SEMIHARMONIC4
LS refinement shellResolution: 3.1→3.47 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.2419 64 5.08 %
Rwork0.1951 1196 -
all0.1975 1260 -
obs--31.65 %
Refinement TLS params.Method: refined / Origin x: -468.133 Å / Origin y: 289.3662 Å / Origin z: 4.302 Å
111213212223313233
T-0.3258 Å2-0.0982 Å2-0.0199 Å2-0.127 Å20.0768 Å2---0.3757 Å2
L2.7422 °20.0453 °2-0.0679 °2-2.1312 °20.111 °2--3.6344 °2
S-0.113 Å °0.1016 Å °0.2185 Å °-0.0234 Å °-0.0348 Å °-0.6523 Å °-0.2443 Å °1.0947 Å °0.1478 Å °
Refinement TLS groupSelection details: { B|* }

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