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- PDB-1txf: CRYSTAL STRUCTURE OF THE GLUR5 LIGAND BINDING CORE IN COMPLEX WIT... -

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Basic information

Entry
Database: PDB / ID: 1txf
TitleCRYSTAL STRUCTURE OF THE GLUR5 LIGAND BINDING CORE IN COMPLEX WITH GLUTAMATE AT 2.1 ANGSTROM RESOLUTION
ComponentsGlutamate receptor, ionotropic kainate 1
KeywordsMEMBRANE PROTEIN
Function / homology
Function and homology information


negative regulation of synaptic transmission, GABAergic / gamma-aminobutyric acid secretion / 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 / regulation of short-term neuronal synaptic plasticity / negative regulation of synaptic transmission, glutamatergic / glutamate binding ...negative regulation of synaptic transmission, GABAergic / gamma-aminobutyric acid secretion / 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 / regulation of short-term neuronal synaptic plasticity / negative regulation of synaptic transmission, glutamatergic / glutamate binding / inhibitory postsynaptic potential / synaptic transmission, GABAergic / adult behavior / behavioral response to pain / kainate selective glutamate receptor activity / modulation of excitatory postsynaptic potential / extracellularly glutamate-gated ion channel activity / ionotropic glutamate receptor complex / membrane depolarization / glutamate-gated receptor activity / glutamate-gated calcium ion channel activity / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / presynaptic modulation of chemical synaptic transmission / ionotropic glutamate receptor signaling pathway / SNARE binding / positive regulation of synaptic transmission, GABAergic / regulation of membrane potential / excitatory postsynaptic potential / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / synaptic transmission, glutamatergic / establishment of localization in cell / postsynaptic density membrane / modulation of chemical synaptic transmission / regulation of synaptic plasticity / terminal bouton / nervous system development / presynaptic membrane / scaffold protein binding / chemical synaptic transmission / postsynaptic membrane / receptor complex / postsynaptic density / neuronal cell body / dendrite / synapse / glutamatergic synapse / identical protein binding / membrane / plasma membrane
Similarity search - Function
Ionotropic glutamate receptor, metazoa / Ligated ion channel L-glutamate- and glycine-binding site / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / Ligated ion channel L-glutamate- and glycine-binding site / Ligand-gated ion channel / : / 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 / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / Ligated ion channel L-glutamate- and glycine-binding site / Ligand-gated ion channel / : / 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
GLUTAMIC ACID / Glutamate receptor ionotropic, kainate 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsMayer, M.L.
CitationJournal: Neuron / Year: 2005
Title: Crystal structures of the GluR5 and GluR6 ligand binding cores: Molecular mechanisms underlying kainate receptor selectivity
Authors: Mayer, M.L.
History
DepositionJul 4, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 8, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 26, 2017Group: Source and taxonomy / Category: entity_src_gen
Revision 1.4Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999SEQUENCE THE NATIVE GLUR-5 IS A MEMBRANE PROTEIN. THE PROTEIN CRYSTALLIZED BY THE AUTHOR IS THE ...SEQUENCE THE NATIVE GLUR-5 IS A MEMBRANE PROTEIN. THE PROTEIN CRYSTALLIZED BY THE AUTHOR IS THE EXTRACELLULAR LIGAND BINDING DOMAIN OF GLUR-5. TRANSMEMBRANE REGIONS WERE GENETICALLY REMOVED AND REPLACED WITH A GLY-THR LINKER. THE SEQUENCE, AS A RESULT, MATCHES DISCONTINUOUSLY WITH THE REFERENCE DATABASE
Remark 300BIOMOLECULE THE BIOLOGICAL UNIT IS BELIEVED TO BE A HETEROTETRAMER, THERE IS ONLY ONE MOLECULE IN ...BIOMOLECULE THE BIOLOGICAL UNIT IS BELIEVED TO BE A HETEROTETRAMER, THERE IS ONLY ONE MOLECULE IN THE ASYMMETRIC UNIT AND SYMMETRY OPERATIONS CANNOT BE APPLIED TO GENERATE THE TETRAMER.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glutamate receptor, ionotropic kainate 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,4012
Polymers29,2541
Non-polymers1471
Water1,67593
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)119.809, 63.710, 50.354
Angle α, β, γ (deg.)90.00, 107.22, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Glutamate receptor, ionotropic kainate 1 / Glutamate receptor 5 / GluR-5 / GluR5


Mass: 29253.566 Da / Num. of mol.: 1
Fragment: GluR5 ligand binding core (sequence database 446-559 and 682-821)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Grik1 / Plasmid: pET22 (modified) / Production host: Escherichia coli (E. coli) / Strain (production host): ORIGAMI B (DE3) / References: UniProt: P22756
#2: Chemical ChemComp-GLU / GLUTAMIC ACID


Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H9NO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 93 / Source method: isolated from a natural source / Formula: H2O

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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: 3.1 Å3/Da / Density % sol: 60.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20% PEG 10K, 100 mM HEPES, 20 mM NaCl, 1 mM EDTA, 10 mM Glutamate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.99997 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 1, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99997 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 21345 / Num. obs: 21345 / % possible obs: 84.3 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 2 / Redundancy: 2.5 % / Biso Wilson estimate: 39.9 Å2 / Rmerge(I) obs: 0.045 / Net I/σ(I): 12.7
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.269 / Mean I/σ(I) obs: 2.2 / Num. unique all: 1042 / % possible all: 49.7

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1S7Y

1s7y


Resolution: 2.1→32.4 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1282416.77 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.25 1226 6.8 %RANDOM
Rwork0.219 ---
all0.222 17941 --
obs0.219 17941 84.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 44.2134 Å2 / ksol: 0.3641 e/Å3
Displacement parametersBiso mean: 41.8 Å2
Baniso -1Baniso -2Baniso -3
1-3.84 Å20 Å2-0.21 Å2
2--5.43 Å20 Å2
3----9.27 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.28 Å
Luzzati d res low-50 Å
Luzzati sigma a0.27 Å0.24 Å
Refinement stepCycle: LAST / Resolution: 2.1→32.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1984 0 10 93 2087
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d22
X-RAY DIFFRACTIONc_improper_angle_d0.84
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.315 128 6.7 %
Rwork0.28 1791 -
obs--54.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP

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