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

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Basic information

Entry
Database: PDB / ID: 5llm
TitleStructure of the thermostabilized EAAT1 cryst 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 / glutamine secretion / membrane protein complex / L-glutamine import across plasma membrane / neurotransmitter uptake / L-serine transmembrane transporter activity / glutamine transport / L-glutamine transmembrane transporter activity ...Defective SLC1A3 causes episodic ataxia 6 (EA6) / auditory behavior / Astrocytic Glutamate-Glutamine Uptake And Metabolism / glutamine secretion / membrane protein complex / L-glutamine import across plasma membrane / neurotransmitter uptake / L-serine transmembrane transporter activity / glutamine transport / L-glutamine transmembrane transporter activity / cranial nerve development / cell morphogenesis involved in neuron differentiation / ligand-gated channel activity / gamma-aminobutyric acid biosynthetic process / 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 / amino acid transmembrane transporter activity / D-aspartate import across plasma membrane / Amino acid transport across the plasma membrane / neutral L-amino acid transmembrane transporter activity / L-aspartate transmembrane transporter activity / L-aspartate import across plasma membrane / Glutamate Neurotransmitter Release Cycle / L-glutamate import across plasma membrane / symporter activity / intracellular sodium ion homeostasis / amino acid transport / neurotransmitter transport / transepithelial transport / antiporter activity / 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 / basal plasma membrane / erythrocyte differentiation / sensory perception of sound / response to wounding / melanosome / virus receptor activity / signaling receptor activity / chemical synaptic transmission / cytoplasmic vesicle / 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: 3.25 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 27, 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)57,0914
Polymers56,5121
Non-polymers5793
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area18870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.270, 123.270, 89.870
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): embryonic / Cell line (production host): HEK-293.2sus / Production host: Homo sapiens (human) / Tissue (production host): embryonic 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: 64.8 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging 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: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 16, 2016
RadiationMonochromator: channel cut monochromator crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.25→45.89 Å / Num. obs: 12338 / % possible obs: 100 % / Redundancy: 27.1 % / Biso Wilson estimate: 135.93 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.2 / Net I/σ(I): 11.7
Reflection shellResolution: 3.25→3.34 Å / Redundancy: 26.9 % / Rmerge(I) obs: 6.772 / Mean I/σ(I) obs: 0.7 / CC1/2: 0.22 / Rpim(I) all: 1.333 / % possible all: 100

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Processing

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

2nwx


Resolution: 3.25→34.5 Å / Cor.coef. Fo:Fc: 0.8695 / Cor.coef. Fo:Fc free: 0.8651 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.446
RfactorNum. reflection% reflectionSelection details
Rfree0.24 474 4.79 %RANDOM
Rwork0.2194 ---
obs0.2204 9888 80.18 %-
Displacement parametersBiso mean: 130.3 Å2
Baniso -1Baniso -2Baniso -3
1-4.8862 Å20 Å20 Å2
2--4.8862 Å20 Å2
3----9.7723 Å2
Refine analyzeLuzzati coordinate error obs: 0.466 Å
Refinement stepCycle: 1 / Resolution: 3.25→34.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3027 0 42 0 3069
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0093108HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.064223HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1059SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes50HARMONIC2
X-RAY DIFFRACTIONt_gen_planes476HARMONIC5
X-RAY DIFFRACTIONt_it3108HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion1.95
X-RAY DIFFRACTIONt_other_torsion20.83
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_contact3888SEMIHARMONIC4
LS refinement shellResolution: 3.25→3.63 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.2297 58 4.25 %
Rwork0.2036 1307 -
all0.2047 1365 -
obs--39.11 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.5586-0.3130.05662.45790.00923.0567-0.02470.0534-0.3764-0.1129-0.0889-0.1520.65010.45540.1136-0.02870.07740.0036-0.1596-0.013-0.4171-54.2504446.0964-4.1214
25.5903-0.7952-0.35433.21220.74521.1273-0.06870.4068-0.4134-0.06540.02-0.76770.38570.78460.0487-0.08390.29150.07220.04950.0887-0.3181-37.801442.1112-5.0307
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{A|37 - 111 A|171 - 283}
2X-RAY DIFFRACTION2{A|112 - 147 A|291 - 487}

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