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- PDB-1wvj: Exploring the GluR2 ligand-binding core in complex with the bicyc... -

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Basic information

Entry
Database: PDB / ID: 1wvj
TitleExploring the GluR2 ligand-binding core in complex with the bicyclic AMPA analogue (S)-4-AHCP
Componentsionotropic glutamate receptor 2
KeywordsMEMBRANE PROTEIN / Ionotropic glutamate receptor GluR2 / ligand-binding core / complex with bicyclic AMPA analogue
Function / homology
Function and homology information


regulation of synaptic plasticity by chemical substance / spine synapse / dendritic spine neck / dendritic spine cytoplasm / dendritic spine head / cellular response to amine stimulus / Activation of AMPA receptors / ligand-gated monoatomic cation channel activity / perisynaptic space / Trafficking of GluR2-containing AMPA receptors ...regulation of synaptic plasticity by chemical substance / spine synapse / dendritic spine neck / dendritic spine cytoplasm / dendritic spine head / cellular response to amine stimulus / Activation of AMPA receptors / ligand-gated monoatomic cation channel activity / perisynaptic space / Trafficking of GluR2-containing AMPA receptors / response to lithium ion / AMPA glutamate receptor activity / AMPA glutamate receptor clustering / regulation of receptor recycling / kainate selective glutamate receptor activity / immunoglobulin binding / AMPA glutamate receptor complex / extracellularly glutamate-gated ion channel activity / ionotropic glutamate receptor complex / cellular response to glycine / asymmetric synapse / Unblocking of NMDA receptors, glutamate binding and activation / glutamate receptor binding / positive regulation of synaptic transmission / conditioned place preference / regulation of synaptic transmission, glutamatergic / response to fungicide / cytoskeletal protein binding / extracellular ligand-gated monoatomic ion channel activity / glutamate-gated receptor activity / cellular response to brain-derived neurotrophic factor stimulus / regulation of long-term synaptic depression / glutamate-gated calcium ion channel activity / somatodendritic compartment / presynaptic active zone membrane / ionotropic glutamate receptor binding / ionotropic glutamate receptor signaling pathway / dendrite cytoplasm / dendrite membrane / excitatory synapse / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / positive regulation of excitatory postsynaptic potential / dendritic shaft / synaptic membrane / SNARE binding / PDZ domain binding / establishment of protein localization / synaptic transmission, glutamatergic / protein tetramerization / long-term synaptic potentiation / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / receptor internalization / cerebral cortex development / postsynaptic density membrane / modulation of chemical synaptic transmission / Schaffer collateral - CA1 synapse / terminal bouton / synaptic vesicle membrane / synaptic vesicle / amyloid-beta binding / presynapse / growth cone / signaling receptor activity / scaffold protein binding / presynaptic membrane / chemical synaptic transmission / dendritic spine / perikaryon / postsynaptic membrane / postsynaptic density / neuron projection / external side of plasma membrane / axon / neuronal cell body / dendrite / synapse / protein kinase binding / protein-containing complex binding / glutamatergic synapse / cell surface / endoplasmic reticulum / protein-containing complex / membrane / identical protein binding / plasma membrane
Similarity search - Function
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. / Periplasmic binding protein-like II / Receptor, ligand binding region ...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. / Periplasmic binding protein-like II / Receptor, ligand binding region / Receptor family ligand binding region / D-Maltodextrin-Binding Protein; domain 2 / Periplasmic binding protein-like I / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-IBC / Glutamate receptor 2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsNielsen, B.B. / Pickering, D.S. / Greenwood, J.R. / Brehm, L. / Gajhede, M. / Schousboe, A. / Kastrup, J.S.
Citation
Journal: FEBS J. / Year: 2005
Title: Exploring the GluR2 ligand-binding core in complex with the bicyclical AMPA analogue (S)-4-AHCP
Authors: Nielsen, B.B. / Pickering, D.S. / Greenwood, J.R. / Brehm, L. / 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.K. / 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, Y. / Jin, R. / Gouaux, E.
History
DepositionDec 15, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 26, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Aug 23, 2017Group: Source and taxonomy / Category: entity_src_gen
Revision 1.4Oct 25, 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
Revision 1.5Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ionotropic glutamate receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9287
Polymers29,2221
Non-polymers7076
Water5,567309
1
A: ionotropic glutamate receptor 2
hetero molecules

A: ionotropic glutamate receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,85714
Polymers58,4432
Non-polymers1,41312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Unit cell
Length a, b, c (Å)94.412, 59.467, 47.845
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-3247-

HOH

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Components

#1: Protein ionotropic glutamate receptor 2 / Glutamate receptor 2


Mass: 29221.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Flop ligand-binding core of GluR2(GluR2-S1S2J) / Source: (gene. exp.) Rattus norvegicus (Norway rat) / 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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-IBC / 3-(3-HYDROXY-7,8-DIHYDRO-6H-CYCLOHEPTA[D]ISOXAZOL-4-YL)-L-ALANINE / 2-AMINO-3-(3-HYDROXY-7,8-DIHYDRO-6H-CYCLOHEPTA[D]-4-ISOXAZOLYL)PROPIONIC ACID


Mass: 238.240 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H14N2O4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 309 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.3 Å3/Da / Density % sol: 46.1 %
Crystal growTemperature: 279 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: PEG 3350, phosphate-citrate buffer, lithium sulfate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 279K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.811 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 25, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.811 Å / Relative weight: 1
ReflectionResolution: 1.75→20.08 Å / Num. all: 27472 / Num. obs: 27472 / % possible obs: 99.1 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Biso Wilson estimate: 18.1 Å2 / Rsym value: 0.037 / Net I/σ(I): 26.7
Reflection shellResolution: 1.75→1.78 Å / Mean I/σ(I) obs: 4.1 / Num. unique all: 1333 / Rsym value: 0.227 / % possible all: 96.3

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1M5C

1m5c


Resolution: 1.75→20.08 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.936 / SU B: 2.37 / SU ML: 0.077 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.116 / ESU R Free: 0.117 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: The side chains of the following residues are not fully defined: LYS A4, LYS A21, GLU A24, GLU A27, LYS A50, LYS A52, ARG A64, ALA A66, ASP A67, LYS A69, LYS A82, GLU A125, LYS A129, THR ...Details: The side chains of the following residues are not fully defined: LYS A4, LYS A21, GLU A24, GLU A27, LYS A50, LYS A52, ARG A64, ALA A66, ASP A67, LYS A69, LYS A82, GLU A125, LYS A129, THR A131, GLU A145, ARG A148, ARG A149, LYS A151, LYS A157, ARG A172, GLU A176, LYS A183, LYS A204, LYS A240 and GLU A243.
RfactorNum. reflection% reflectionSelection details
Rfree0.21418 1376 5 %RANDOM
Rwork0.16882 ---
all0.17111 27450 --
obs0.17111 26073 99.08 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 20.624 Å2
Baniso -1Baniso -2Baniso -3
1-0.27 Å20 Å20 Å2
2---1.01 Å20 Å2
3---0.73 Å2
Refinement stepCycle: LAST / Resolution: 1.75→20.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2039 0 45 309 2393
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0222154
X-RAY DIFFRACTIONr_angle_refined_deg1.5991.9992891
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7465261
X-RAY DIFFRACTIONr_chiral_restr0.1130.2310
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021557
X-RAY DIFFRACTIONr_nbd_refined0.210.21043
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1470.2234
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.240.256
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1740.235
X-RAY DIFFRACTIONr_mcbond_it0.9931.51291
X-RAY DIFFRACTIONr_mcangle_it1.70622078
X-RAY DIFFRACTIONr_scbond_it2.9243863
X-RAY DIFFRACTIONr_scangle_it4.754.5813
LS refinement shellResolution: 1.754→1.8 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.318 98 -
Rwork0.248 1833 -
obs-1833 96.5 %

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