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- PDB-2wky: Crystal structure of the ligand-binding core of GluR5 in complex ... -

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Basic information

Entry
Database: PDB / ID: 2wky
TitleCrystal structure of the ligand-binding core of GluR5 in complex with the agonist 4-AHCP
ComponentsGLUTAMATE RECEPTOR, IONOTROPIC KAINATE 1
KeywordsMEMBRANE PROTEIN / SYNAPSE / MEMBRANE / RECEPTOR / TRANSPORT / ION CHANNEL / RNA EDITING / GLYCOPROTEIN / CELL JUNCTION / IONOTROPIC GLUTAMATE RECEPTOR / ALTERNATIVE SPLICING / POSTSYNAPTIC CELL MEMBRANE / IONIC CHANNEL / CELL MEMBRANE / ION TRANSPORT / TRANSMEMBRANE / PHOSPHOPROTEIN / LIGAND-BINDING CORE
Function / homology
Function and homology information


gamma-aminobutyric acid secretion / negative regulation of synaptic transmission, GABAergic / L-glutamate transmembrane transporter activity / positive regulation of gamma-aminobutyric acid secretion / Activation of Na-permeable kainate receptors / kainate selective glutamate receptor complex / Activation of Ca-permeable Kainate Receptor / negative regulation of synaptic transmission, glutamatergic / regulation of short-term neuronal synaptic plasticity / inhibitory postsynaptic potential ...gamma-aminobutyric acid secretion / negative regulation of synaptic transmission, GABAergic / L-glutamate transmembrane transporter activity / positive regulation of gamma-aminobutyric acid secretion / Activation of Na-permeable kainate receptors / kainate selective glutamate receptor complex / Activation of Ca-permeable Kainate Receptor / negative regulation of synaptic transmission, glutamatergic / regulation of short-term neuronal synaptic plasticity / inhibitory postsynaptic potential / synaptic transmission, GABAergic / glutamate binding / adult behavior / modulation of excitatory postsynaptic potential / behavioral response to pain / membrane depolarization / kainate selective glutamate receptor activity / ionotropic glutamate receptor complex / extracellularly glutamate-gated ion channel activity / glutamate-gated receptor activity / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / excitatory postsynaptic potential / presynaptic modulation of chemical synaptic transmission / regulation of membrane potential / ionotropic glutamate receptor signaling pathway / SNARE binding / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / synaptic transmission, glutamatergic / establishment of localization in cell / positive regulation of synaptic transmission, GABAergic / postsynaptic density membrane / regulation of synaptic plasticity / modulation of chemical synaptic transmission / terminal bouton / presynaptic membrane / nervous system development / chemical synaptic transmission / scaffold protein binding / postsynaptic density / receptor complex / neuronal cell body / dendrite / synapse / glutamatergic synapse / membrane / identical protein binding / plasma membrane
Similarity search - Function
Ionotropic glutamate receptor, metazoa / Ligated ion channel L-glutamate- and glycine-binding site / : / Ligand-gated ion channel / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / Ligated ion channel L-glutamate- and glycine-binding site / Ionotropic glutamate receptor / Eukaryotic homologues of bacterial periplasmic substrate binding proteins. / Receptor, ligand binding region / Receptor family ligand binding region ...Ionotropic glutamate receptor, metazoa / Ligated ion channel L-glutamate- and glycine-binding site / : / Ligand-gated ion channel / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / Ligated ion channel L-glutamate- and glycine-binding site / Ionotropic glutamate receptor / Eukaryotic homologues of bacterial periplasmic substrate binding proteins. / Receptor, ligand binding region / Receptor family ligand binding region / Periplasmic binding protein-like II / Periplasmic binding protein-like I / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-IBC / Glutamate receptor ionotropic, kainate 1
Similarity search - Component
Biological speciesRATTUS NORVEGICUS (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsNaur, P. / Gajhede, M. / Kastrup, J.S.
CitationJournal: J.Med.Chem. / Year: 2009
Title: The Glutamate Receptor Glur5 Agonist (S)-2-Amino-3-(3-Hydroxy-7,8-Dihydro-6H-Cyclohepta[D]Isoxazol-4-Yl)Propionic Acid and the 8-Methyl Analogue: Synthesis, Molecular Pharmacology, and ...Title: The Glutamate Receptor Glur5 Agonist (S)-2-Amino-3-(3-Hydroxy-7,8-Dihydro-6H-Cyclohepta[D]Isoxazol-4-Yl)Propionic Acid and the 8-Methyl Analogue: Synthesis, Molecular Pharmacology, and Biostructural Characterization
Authors: Clausen, R.P. / Naur, P. / Kristensen, A.S. / Greenwood, J.R. / Strange, M. / Brauner-Osborne, H. / Jensen, A.A. / Nielsen, A.S. / Geneser, U. / Ringgaard, L.M. / Nielsen, B. / Pickering, D. ...Authors: Clausen, R.P. / Naur, P. / Kristensen, A.S. / Greenwood, J.R. / Strange, M. / Brauner-Osborne, H. / Jensen, A.A. / Nielsen, A.S. / Geneser, U. / Ringgaard, L.M. / Nielsen, B. / Pickering, D.S. / Brehm, L. / Gajhede, M. / Krogsgaard-Larsen, P. / Kastrup, J.S.
History
DepositionJun 18, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 21, 2009Provider: repository / Type: Initial release
Revision 1.1Jun 30, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.type
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GLUTAMATE RECEPTOR, IONOTROPIC KAINATE 1
B: GLUTAMATE RECEPTOR, IONOTROPIC KAINATE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,0236
Polymers58,4752
Non-polymers5474
Water5,314295
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3410 Å2
ΔGint-21 kcal/mol
Surface area23240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.310, 71.310, 234.958
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein GLUTAMATE RECEPTOR, IONOTROPIC KAINATE 1 / / GLUTAMATE RECEPTOR 5 / GLUR-5 / GLUR5


Mass: 29237.566 Da / Num. of mol.: 2 / Fragment: LIGAND-BINDING CORE, RESIDUES 430-544,667-806
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) RATTUS NORVEGICUS (Norway rat) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ORIGAMI B / References: UniProt: P22756
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-IBC / 3-(3-HYDROXY-7,8-DIHYDRO-6H-CYCLOHEPTA[D]ISOXAZOL-4-YL)-L-ALANINE / 2-AMINO-3-(3-HYDROXY-7,8-DIHYDRO-6H-CYCLOHEPTA[D]-4-ISOXAZOLYL)PROPIONIC ACID


Mass: 238.240 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H14N2O4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 295 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE CRYSTALLIZED PROTEIN CONSISTS OF GLY RESIDUE FOLLOWED BY RESIDUE 430-544 AND 667-805 FROM THE ...THE CRYSTALLIZED PROTEIN CONSISTS OF GLY RESIDUE FOLLOWED BY RESIDUE 430-544 AND 667-805 FROM THE INTACT RECEPTOR LINKED BY A GLY-THR DIPEPTIDE. THERE IS A SEQUENCE CONFLICT AT RESIDUE 34 OF THE CRYSTALLIZED PROTEIN DUE TO DIFFERENCES IN DATABASE SEQUENCE (SEE GENBANK ACCESION NO. AAA02874).

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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: 2.6 Å3/Da / Density % sol: 52 % / Description: NONE
Crystal growDetails: 18 % PEG4000 0.3 M LI2SO4 0.1 M TRIS-HCL PH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 6, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.2→30 Å / Num. obs: 31679 / % possible obs: 99.4 % / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Biso Wilson estimate: 18.8 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 12.6
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 2.6 / % possible all: 99.3

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2PBW

2pbw


Resolution: 2.2→29.54 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 2547573.64 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.248 1569 5 %RANDOM
Rwork0.211 ---
obs0.211 31666 99.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 27.0097 Å2 / ksol: 0.345161 e/Å3
Displacement parametersBiso mean: 27.4 Å2
Baniso -1Baniso -2Baniso -3
1-1.57 Å20 Å20 Å2
2--1.57 Å20 Å2
3----3.15 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.29 Å0.24 Å
Refinement stepCycle: LAST / Resolution: 2.2→29.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4042 0 36 295 4373
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.97
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Refine LS restraints NCSNCS model details: NONE
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.316 237 4.6 %
Rwork0.256 4864 -
obs--98.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION44-AHCP.PAR4-AHCP.TOP

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