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- PDB-8i0b: The crystal structure of human glutamate receptor 2 in complex wi... -

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Basic information

Entry
Database: PDB / ID: 8i0b
TitleThe crystal structure of human glutamate receptor 2 in complex with LT-102
ComponentsGlutamate receptor 2,Isoform Flip of Glutamate receptor 2
KeywordsSTRUCTURAL PROTEIN / glutamate receptor 2 / inhibitor / complex
Function / homology
Function and homology information


Activation of AMPA receptors / Activation of AMPA receptors / postsynaptic endocytic zone / Unblocking of NMDA receptors, glutamate binding and activation / Trafficking of GluR2-containing AMPA receptors / Trafficking of GluR2-containing AMPA receptors / spine synapse / dendritic spine neck / dendritic spine head / perisynaptic space ...Activation of AMPA receptors / Activation of AMPA receptors / postsynaptic endocytic zone / Unblocking of NMDA receptors, glutamate binding and activation / Trafficking of GluR2-containing AMPA receptors / Trafficking of GluR2-containing AMPA receptors / spine synapse / dendritic spine neck / dendritic spine head / perisynaptic space / cellular response to glycine / Unblocking of NMDA receptors, glutamate binding and activation / AMPA glutamate receptor activity / immunoglobulin binding / Long-term potentiation / AMPA glutamate receptor complex / kainate selective glutamate receptor activity / excitatory synapse / extracellularly glutamate-gated ion channel activity / asymmetric synapse / regulation of receptor recycling / glutamate receptor binding / positive regulation of synaptic transmission / presynaptic active zone membrane / MECP2 regulates neuronal receptors and channels / glutamate-gated receptor activity / 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 / cytoskeletal protein binding / dendrite cytoplasm / SNARE binding / dendritic shaft / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / synaptic membrane / synaptic transmission, glutamatergic / PDZ domain binding / protein tetramerization / postsynaptic density membrane / modulation of chemical synaptic transmission / Schaffer collateral - CA1 synapse / establishment of protein localization / terminal bouton / receptor internalization / synaptic vesicle membrane / endocytic vesicle membrane / synaptic vesicle / presynapse / signaling receptor activity / presynaptic membrane / amyloid-beta binding / growth cone / perikaryon / chemical synaptic transmission / postsynapse / scaffold protein binding / postsynaptic membrane / dendritic spine / postsynaptic density / neuron projection / axon / external side of plasma membrane / neuronal cell body / dendrite / synapse / glutamatergic synapse / protein-containing complex binding / endoplasmic reticulum membrane / protein kinase binding / cell surface / endoplasmic reticulum / signal transduction / 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 I
Similarity search - Domain/homology
: / Glutamate receptor 2 / Glutamate receptor 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.73 Å
AuthorsQi, X.Y. / Wu, C.Y.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Structure of the human GluA2 LBD in complex with LT-102
Authors: Qi, X.Y. / Wu, C.Y.
History
DepositionJan 10, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 7, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glutamate receptor 2,Isoform Flip of Glutamate receptor 2
B: Glutamate receptor 2,Isoform Flip of Glutamate receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,0299
Polymers66,2312
Non-polymers7987
Water6,864381
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2950 Å2
ΔGint-79 kcal/mol
Surface area23250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.400, 47.104, 98.413
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21221

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Glutamate receptor 2,Isoform Flip of Glutamate receptor 2 / GluR-2 / AMPA-selective glutamate receptor 2 / GluR-B / GluR-K2 / Glutamate receptor ionotropic / ...GluR-2 / AMPA-selective glutamate receptor 2 / GluR-B / GluR-K2 / Glutamate receptor ionotropic / AMPA 2 / GluA2


Mass: 33115.305 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse), (gene. exp.) Homo sapiens (human)
Gene: Gria2, Glur2, GRIA2, GLUR2 / Production host: Escherichia coli (E. coli) / References: UniProt: P23819, UniProt: P42262

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Non-polymers , 5 types, 388 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-NXO / 8-[4-(2-fluorophenyl)phenyl]-3,4-dihydro-1,2$l^{6},3-benzoxathiazine 2,2-dioxide


Mass: 355.383 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H14FNO3S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 381 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.12 Å3/Da / Density % sol: 42.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 22% PEG 8000, 0.1M NaAC pH 5.0, 0.2M (NH4)2SO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.978 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Nov 26, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.73→98.41 Å / Num. obs: 59162 / % possible obs: 98.8 % / Redundancy: 12 % / CC1/2: 0.999 / Rmerge(I) obs: 0.097 / Net I/σ(I): 15
Reflection shellResolution: 1.73→1.82 Å / Num. unique obs: 8326 / CC1/2: 0.895

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Processing

Software
NameVersionClassification
PHENIXv1.2refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.73→42.49 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2781 1998 3.38 %
Rwork0.2206 --
obs0.2225 59077 98.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.73→42.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4056 0 47 381 4484
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_dihedral_angle_d6.648585
X-RAY DIFFRACTIONf_chiral_restr0.062623
X-RAY DIFFRACTIONf_plane_restr0.01710
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.73-1.770.3611360.30663876X-RAY DIFFRACTION95
1.77-1.820.39291400.29293975X-RAY DIFFRACTION97
1.82-1.870.33531390.27474002X-RAY DIFFRACTION98
1.87-1.930.3421410.26624006X-RAY DIFFRACTION98
1.93-20.33391420.25294048X-RAY DIFFRACTION99
2-2.080.31661410.23984015X-RAY DIFFRACTION99
2.08-2.180.28321410.23844070X-RAY DIFFRACTION99
2.18-2.290.27891420.23544067X-RAY DIFFRACTION99
2.29-2.440.33571420.24244073X-RAY DIFFRACTION99
2.44-2.620.32281440.23934118X-RAY DIFFRACTION99
2.62-2.890.30561440.23074090X-RAY DIFFRACTION99
2.89-3.30.26741440.21184153X-RAY DIFFRACTION99
3.31-4.160.2211480.1784202X-RAY DIFFRACTION99

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