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- PDB-1gr2: STRUCTURE OF A GLUTAMATE RECEPTOR LIGAND BINDING CORE (GLUR2) COM... -

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Basic information

Entry
Database: PDB / ID: 1gr2
TitleSTRUCTURE OF A GLUTAMATE RECEPTOR LIGAND BINDING CORE (GLUR2) COMPLEXED WITH KAINATE
ComponentsPROTEIN (GLUTAMATE RECEPTOR 2)
KeywordsMEMBRANE PROTEIN / EXCITORY NEUROTRANSMITTER RECEPTOR / GLUTAMATE RECEPTOR
Function / homology
Function and homology information


spine synapse / dendritic spine neck / dendritic spine head / Activation of AMPA receptors / perisynaptic space / AMPA glutamate receptor activity / Trafficking of GluR2-containing AMPA receptors / response to lithium ion / immunoglobulin binding / AMPA glutamate receptor complex ...spine synapse / dendritic spine neck / dendritic spine head / Activation of AMPA receptors / perisynaptic space / AMPA glutamate receptor activity / Trafficking of GluR2-containing AMPA receptors / response to lithium ion / immunoglobulin binding / AMPA glutamate receptor complex / kainate selective glutamate receptor activity / ionotropic glutamate receptor complex / extracellularly glutamate-gated ion channel activity / cellular response to glycine / asymmetric synapse / regulation of receptor recycling / Unblocking of NMDA receptors, glutamate binding and activation / glutamate receptor binding / positive regulation of synaptic transmission / glutamate-gated receptor activity / presynaptic active zone membrane / response to fungicide / regulation of synaptic transmission, glutamatergic / somatodendritic compartment / cellular response to brain-derived neurotrophic factor stimulus / dendrite membrane / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / cytoskeletal protein binding / ionotropic glutamate receptor signaling pathway / dendrite cytoplasm / SNARE binding / dendritic shaft / synaptic membrane / synaptic transmission, glutamatergic / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / PDZ domain binding / protein tetramerization / postsynaptic density membrane / ionotropic glutamate receptor binding / Schaffer collateral - CA1 synapse / modulation of chemical synaptic transmission / establishment of protein localization / receptor internalization / terminal bouton / cerebral cortex development / synaptic vesicle membrane / synaptic vesicle / presynapse / presynaptic membrane / signaling receptor activity / amyloid-beta binding / growth cone / scaffold protein binding / chemical synaptic transmission / postsynaptic membrane / perikaryon / dendritic spine / postsynaptic density / neuron projection / axon / neuronal cell body / glutamatergic synapse / synapse / dendrite / protein-containing complex binding / endoplasmic reticulum membrane / protein kinase binding / cell surface / endoplasmic reticulum / protein-containing complex / identical protein binding / membrane / plasma membrane
Similarity search - Function
Bacterial extracellular solute-binding proteins, family 3 / Solute-binding protein family 3/N-terminal domain of MltF / 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. ...Bacterial extracellular solute-binding proteins, family 3 / Solute-binding protein family 3/N-terminal domain of MltF / 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
3-(CARBOXYMETHYL)-4-ISOPROPENYLPROLINE / Glutamate receptor 2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / MAD / Resolution: 1.9 Å
AuthorsArmstrong, N. / Sun, Y. / Chen, G.Q. / Gouaux, E.
CitationJournal: Nature / Year: 1998
Title: Structure of a glutamate-receptor ligand-binding core in complex with kainate.
Authors: Armstrong, N. / Sun, Y. / Chen, G.Q. / Gouaux, E.
History
DepositionSep 17, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Dec 9, 1998Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN (GLUTAMATE RECEPTOR 2)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,9542
Polymers30,7411
Non-polymers2131
Water3,153175
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.220, 63.070, 46.320
Angle α, β, γ (deg.)90.00, 92.99, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein PROTEIN (GLUTAMATE RECEPTOR 2) / GLUR-B / GLUR-2


Mass: 30741.197 Da / Num. of mol.: 1 / Fragment: LIGAND BINDING DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Description: SYNTHETIC GENE / Organ: BRAIN / Species (production host): Escherichia coli / Cellular location (production host): CYTOPLASM / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P19491
#2: Chemical ChemComp-KAI / 3-(CARBOXYMETHYL)-4-ISOPROPENYLPROLINE / KAINATE


Mass: 213.230 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15NO4 / Comment: neurotransmitter, agonist*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 175 / 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: 2.05 Å3/Da / Density % sol: 38 %
Crystal growpH: 5 / Details: 50 MM KIPI, PH 5.0, 14% PEG 8K
Crystal
*PLUS
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / Details: Chen, G.-Q., (1998) Protein Sci., 7, 2623. / pH: 4.6
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
125 %PEG40001reservoir
20.1 M1reservoirNaOAcpH4.6
30.2 Mammonium sulfate1reservoir
47.5 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceWavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: May 1, 1998 / Details: MIRRORS
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→25 Å / Num. obs: 19209 / % possible obs: 97.2 % / Observed criterion σ(I): 2 / Redundancy: 3.75 % / Rsym value: 0.033

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
X-PLOR3.851refinement
RefinementMethod to determine structure: MAD / Resolution: 1.9→6 Å / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.273 1400 8 %RANDOM
Rwork0.216 ---
obs0.216 19483 95 %-
Displacement parametersBiso mean: 18.86 Å2
Refinement stepCycle: LAST / Resolution: 1.9→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1870 0 0 175 2045
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.483
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
σ(F): 2 / % reflection Rfree: 8 %
Solvent computation
*PLUS
Displacement parameters
*PLUS

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