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- PDB-5llu: Structure of the thermostabilized EAAT1 cryst-II mutant in comple... -

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Basic information

Entry
Database: PDB / ID: 5llu
TitleStructure of the thermostabilized EAAT1 cryst-II mutant in complex with L-ASP
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 / thermostabilized
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
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: 3.32 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 28, 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)56,6163
Polymers56,4601
Non-polymers1562
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)169,8499
Polymers169,3813
Non-polymers4686
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area8070 Å2
ΔGint-61 kcal/mol
Surface area47950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.320, 123.320, 89.570
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
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-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


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

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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: 30% PEG400, 100 mM Tris pH 8.2, 50 mM Calcium chloride, 50 mM Barium chloride
PH range: 8-8.4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.009 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 19, 2016
RadiationMonochromator: Channel-cut Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.009 Å / Relative weight: 1
ReflectionResolution: 3.32→45.87 Å / Num. all: 326273 / Num. obs: 11556 / % possible obs: 100 % / Redundancy: 28.2 % / Biso Wilson estimate: 137.12 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.15 / Net I/σ(I): 13
Reflection shellResolution: 3.32→3.85 Å / Redundancy: 26.2 % / Rmerge(I) obs: 8.031 / CC1/2: 0.313 / % possible all: 100

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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: 3.32→20 Å / Cor.coef. Fo:Fc: 0.9287 / Cor.coef. Fo:Fc free: 0.8871 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.494
RfactorNum. reflection% reflectionSelection details
Rfree0.2541 445 4.81 %RANDOM
Rwork0.2073 ---
obs0.2096 9251 80.44 %-
Displacement parametersBiso mean: 137.2 Å2
Baniso -1Baniso -2Baniso -3
1-5.4518 Å20 Å20 Å2
2--5.4518 Å20 Å2
3----10.9036 Å2
Refine analyzeLuzzati coordinate error obs: 0.464 Å
Refinement stepCycle: 1 / Resolution: 3.32→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3007 0 10 0 3017
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0093048HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.054139HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1042SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes52HARMONIC2
X-RAY DIFFRACTIONt_gen_planes438HARMONIC5
X-RAY DIFFRACTIONt_it3048HARMONIC20
X-RAY DIFFRACTIONt_nbd2SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion1.9
X-RAY DIFFRACTIONt_other_torsion20.69
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion432SEMIHARMONIC5
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_contact3927SEMIHARMONIC4
LS refinement shellResolution: 3.32→3.71 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.2294 50 3.85 %
Rwork0.1988 1249 -
all0.1999 1299 -
obs--40.07 %
Refinement TLS params.Method: refined / Origin x: 7.7803 Å / Origin y: 47.6181 Å / Origin z: 0.0854 Å
111213212223313233
T0.1572 Å20.1343 Å20.0509 Å2--0.282 Å20.0347 Å2---0.4424 Å2
L2.2983 °2-0.5526 °20.3356 °2-3.3609 °2-0.7569 °2--3.3898 °2
S-0.0298 Å °-0.0387 Å °-0.65 Å °0.1213 Å °-0.0861 Å °-0.0701 Å °1.1128 Å °0.2496 Å °0.1159 Å °
Refinement TLS groupSelection details: { *|* }

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