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- PDB-1mxu: CRYSTAL STRUCTURE OF THE GLUR2 LIGAND BINDING CORE (S1S2J) in com... -

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Basic information

Entry
Database: PDB / ID: 1mxu
TitleCRYSTAL STRUCTURE OF THE GLUR2 LIGAND BINDING CORE (S1S2J) in complex with bromo-willardiine (Control for the crystal titration experiments)
ComponentsGLUTAMATE RECEPTOR 2GRIA2
KeywordsMEMBRANE PROTEIN / IONOTROPIC GLUTAMATE RECEPTOR / GLUR2 / LIGAND BINDING CORE / S1S2 / PARTIAL AGONIST / Bromo-WILLARDIINE / AMPA / crystal titration
Function / homology
Function and homology information


spine synapse / dendritic spine neck / dendritic spine head / Activation of AMPA receptors / response to lithium ion / perisynaptic space / cellular response to glycine / AMPA glutamate receptor activity / Trafficking of GluR2-containing AMPA receptors / immunoglobulin binding ...spine synapse / dendritic spine neck / dendritic spine head / Activation of AMPA receptors / response to lithium ion / perisynaptic space / cellular response to glycine / AMPA glutamate receptor activity / Trafficking of GluR2-containing AMPA receptors / immunoglobulin binding / AMPA glutamate receptor complex / kainate selective glutamate receptor activity / ionotropic glutamate receptor complex / extracellularly glutamate-gated ion channel activity / 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 / cellular response to brain-derived neurotrophic factor stimulus / somatodendritic compartment / dendrite membrane / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / ionotropic glutamate receptor binding / ionotropic glutamate receptor signaling pathway / dendrite cytoplasm / cytoskeletal protein binding / SNARE binding / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / dendritic shaft / synaptic membrane / synaptic transmission, glutamatergic / PDZ domain binding / postsynaptic density membrane / protein tetramerization / modulation of chemical synaptic transmission / Schaffer collateral - CA1 synapse / establishment of protein localization / terminal bouton / receptor internalization / synaptic vesicle membrane / cerebral cortex development / synaptic vesicle / presynapse / signaling receptor activity / presynaptic membrane / amyloid-beta binding / growth cone / perikaryon / chemical synaptic transmission / scaffold protein binding / postsynaptic membrane / dendritic spine / postsynaptic density / neuron projection / axon / neuronal cell body / dendrite / synapse / glutamatergic synapse / protein-containing complex binding / endoplasmic reticulum membrane / protein kinase binding / cell surface / endoplasmic reticulum / protein-containing complex / membrane / identical protein binding / 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
Chem-BWD / Glutamate receptor 2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.8 Å
AuthorsJin, R. / Gouaux, E.
Citation
Journal: Biochemistry / Year: 2003
Title: Probing the Function, Conformational Plasticity, and Dimer-Dimer Contacts of the GluR2 Ligand-Binding Core: Studies of 5-Substituted Willardiines and GluR2 S1S2 in the Crystal
Authors: Jin, R. / Gouaux, E.
#1: Journal: To be Published
Title: PARTIAL AGONIST ACTION DEFINED BY STABILIZATION OF SPECIFIC CONFORMATIONAL SUBSTATES
Authors: Jin, R. / Bank, T. / Mayer, M.L. / Traynelis, S. / Gouaux, E.
History
DepositionOct 3, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 10, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 23, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GLUTAMATE RECEPTOR 2
B: GLUTAMATE RECEPTOR 2
C: GLUTAMATE RECEPTOR 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,82611
Polymers87,6653
Non-polymers1,1618
Water11,620645
1
A: GLUTAMATE RECEPTOR 2
C: GLUTAMATE RECEPTOR 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,1967
Polymers58,4432
Non-polymers7525
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: GLUTAMATE RECEPTOR 2
hetero molecules

B: GLUTAMATE RECEPTOR 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,2618
Polymers58,4432
Non-polymers8186
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Buried area2960 Å2
ΔGint-102 kcal/mol
Surface area22740 Å2
MethodPISA, PQS
3
C: GLUTAMATE RECEPTOR 2
hetero molecules

A: GLUTAMATE RECEPTOR 2
B: GLUTAMATE RECEPTOR 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,82611
Polymers87,6653
Non-polymers1,1618
Water543
TypeNameSymmetry operationNumber
crystal symmetry operation4_557x+1/2,-y+1/2,-z+21
identity operation1_555x,y,z1
Buried area3660 Å2
ΔGint-167 kcal/mol
Surface area34360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.292, 163.403, 48.072
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein GLUTAMATE RECEPTOR 2 / GRIA2 / GLUR-2 / GLUR-B / GLUR-K2 / GLUTAMATE RECEPTOR IONOTROPIC / AMPA 2


Mass: 29221.682 Da / Num. of mol.: 3 / Fragment: LIGAND BINDING CORE (S1S2J)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Plasmid: PETGQ / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P19491
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-BWD / 2-AMINO-3-(5-BROMO-2,4-DIOXO-3,4-DIHYDRO-2H-PYRIMIDIN-1-YL)-PROPIONIC ACID / BROMO-WILLARDIINE


Mass: 278.060 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C7H8BrN3O4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 645 / 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: 2.56 Å3/Da / Density % sol: 51.95 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG8K, ammonium sulfate, zinc acetate, BrW and sodium cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 mMHEPES1droppH7.0
220 mM1dropNaCl
31 mMEDTA1drop
410 mg/mlprotein1drop
512-16 %PEG80001reservoir
60.25-0.3 Mammonium sulfate1reservoir
70.05 Mzinc acetate1reservoir
80.1 Msodium cacodylate1reservoirpH6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.91843 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 15, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91843 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. obs: 76525 / % possible obs: 90.2 % / Observed criterion σ(I): -3 / Redundancy: 4.5 % / Biso Wilson estimate: 17.3 Å2 / Rmerge(I) obs: 0.061
Reflection shellResolution: 1.8→1.86 Å / Rmerge(I) obs: 0.203 / % possible all: 55.2
Reflection
*PLUS
Highest resolution: 1.8 Å
Reflection shell
*PLUS
Highest resolution: 1.8 Å / % possible obs: 55.2 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.8→28.37 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 2236837.62 / Data cutoff high rms absF: 2236837.62 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.234 7720 10.1 %RANDOM
Rwork0.211 ---
obs0.211 76525 90.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 60.9094 Å2 / ksol: 0.406692 e/Å3
Displacement parametersBiso mean: 23.6 Å2
Baniso -1Baniso -2Baniso -3
1-0.9 Å20 Å20 Å2
2--0.24 Å20 Å2
3----1.14 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.15 Å0.1 Å
Refinement stepCycle: LAST / Resolution: 1.8→28.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5881 0 50 645 6576
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d21.7
X-RAY DIFFRACTIONc_improper_angle_d0.73
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.266 877 10.4 %
Rwork0.231 7568 -
obs-8445 60.8 %
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 DIFFRACTION4PARA_BR.TESTTOPO_BR.TEST
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.73

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