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- PDB-1syh: X-RAY STRUCTURE OF THE GLUR2 LIGAND-BINDING CORE (S1S2J) IN COMPL... -

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Basic information

Entry
Database: PDB / ID: 1syh
TitleX-RAY STRUCTURE OF THE GLUR2 LIGAND-BINDING CORE (S1S2J) IN COMPLEX WITH (S)-CPW399 AT 1.85 A RESOLUTION.
ComponentsGlutamate receptor 2GRIA2
KeywordsMEMBRANE PROTEIN / IONOTROPIC GLUTAMATE RECEPTOR GLUR2 / LIGAND-BINDING CORE / AGONIST COMPLEX
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-CPW / Glutamate receptor 2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsFrandsen, A. / Pickering, D.S. / Vestergaard, B. / Kasper, C. / Nielsen, B.B. / Greenwood, J.R. / Campiani, G. / Gajhede, M. / Schousboe, A. / Kastrup, J.S.
Citation
Journal: Mol.Pharmacol. / Year: 2005
Title: Tyr702 Is an Important Determinant of Agonist Binding and Domain Closure of the Ligand-Binding Core of GluR2.
Authors: Frandsen, A. / Pickering, D.S. / Vestergaard, B. / Kasper, C. / Nielsen, B.B. / Greenwood, J.R. / Campiani, G. / Fattorusso, C. / Gajhede, M. / Schousboe, A. / Kastrup, J.S.
#1: Journal: J.Mol.Biol. / Year: 2002
Title: STRUCTURAL BASIS FOR AMPA RECEPTOR ACTIVATION AND LIGAND SELECTIVITY: CRYSTAL STRUCTURES OF FIVE AGONIST COMPLEXES WITH THE GLUR2 LIGAND BINDING CORE.
Authors: HOGNER, A. / KASTRUP, J.S. / JIN, R. / LILJEFORS, T. / MAYER, M.L. / EGEBJERG, J. / LARSEN, I. / GOUAUX, E.
#2: Journal: NEURON / Year: 2000
Title: MECHANISMS FOR ACTIVATION AND ANTAGONISM OF AN AMPA-SENSITIVE GLUTAMATE RECEPTOR: CRYSTAL STRUCTURES OF THE GLUR2 LIGAND BINDING CORE.
Authors: ARMSTRONG, N. / GOUAUX, E.
#3: Journal: Protein Sci. / Year: 1998
Title: PROBING THE LIGAND BINDING DOMAIN OF THE GLUR2 RECEPTOR BY PROTEOLYSIS AND DELETION MUTAGENESIS DEFINES DOMAIN BOUNDARIES AND YIELDS A CRYSTALLIZABLE CONSTRUCT.
Authors: CHEN, G.Q. / SUN, R. / JIN, R. / GOUAUX, E.
History
DepositionApr 1, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 22, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 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 / diffrn_source / 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 / _diffrn_source.pdbx_synchrotron_site / _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 TRANSMEMBRANE REGIONS WERE GENETICALLY REMOVED AND REPLACED WITH A GLY-THR LINKER ...SEQUENCE TRANSMEMBRANE REGIONS WERE GENETICALLY REMOVED AND REPLACED WITH A GLY-THR LINKER (RESIDUES 115 AND 116)

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glutamate receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,4612
Polymers29,2221
Non-polymers2391
Water7,584421
1
A: Glutamate receptor 2
hetero molecules

A: Glutamate receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,9224
Polymers58,4432
Non-polymers4782
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Unit cell
Length a, b, c (Å)58.908, 96.353, 48.530
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.: 1 / Fragment: GLUR2-FLOP LIGAND-BINDING CORE (S1S2J)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: GRIA2, GLUR2 / Plasmid: PET30B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P19491
#2: Chemical ChemComp-CPW / (S)-2-AMINO-3-(1,3,5,7-PENTAHYDRO-2,4-DIOXO-CYCLOPENTA[E]PYRIMIDIN-1-YL) PROIONIC ACID


Mass: 239.228 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H13N3O4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 421 / 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: 2.36 Å3/Da / Density % sol: 48 %
Crystal growTemperature: 280 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: PEG8000, cacodylate, (NH4)2SO4 , pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 280K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.8111 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 27, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8111 Å / Relative weight: 1
ReflectionResolution: 1.8→25 Å / Num. all: 26350 / Num. obs: 26350 / % possible obs: 99.3 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 4.2 % / Biso Wilson estimate: 11.3 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 14.8
Reflection shellResolution: 1.8→1.86 Å / Rmerge(I) obs: 0.392 / Mean I/σ(I) obs: 3.5 / Num. unique all: 2611 / % possible all: 100

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1M5C

1m5c


Resolution: 1.8→24.38 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1431157 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED. / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: RESIDUES 1-2 AND 262-263 WERE NOT LOCATED IN THE ELECTRON DENSITY MAP.
RfactorNum. reflection% reflectionSelection details
Rfree0.199 1264 4.8 %Random
Rwork0.176 ---
all-26137 --
obs-26137 99.3 %-
Solvent computationSolvent model: flat model / Bsol: 45.6 Å2 / ksol: 0.39 e/Å3
Displacement parametersBiso mean: 13 Å2
Baniso -1Baniso -2Baniso -3
1-0.27 Å20 Å20 Å2
2---0.07 Å20 Å2
3----0.2 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.19 Å0.17 Å
Luzzati d res low-5 Å
Luzzati sigma a0.11 Å0.07 Å
Refinement stepCycle: LAST / Resolution: 1.8→24.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2072 0 17 421 2510
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d21.7
X-RAY DIFFRACTIONc_improper_angle_d0.89
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.219 196 4.6 %
Rwork0.193 4093 -
obs-4289 100 %

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