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- PDB-2anj: Crystal Structure of the Glur2 Ligand Binding Core (S1S2J-Y450W) ... -

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Basic information

Entry
Database: PDB / ID: 2anj
TitleCrystal Structure of the Glur2 Ligand Binding Core (S1S2J-Y450W) Mutant in Complex With the Partial Agonist Kainic Acid at 2.1 A Resolution
ComponentsGlutamate receptor 2
KeywordsMEMBRANE PROTEIN / Ionotropic Glutamate Receptor / GluR2 Ligand-Binding Core / Agonist Complex / Mutant
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 / terminal bouton / receptor internalization / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsHolm, M.M. / Naur, P. / Vestergaard, B. / Geballe, M.T. / Gajhede, M. / Kastrup, J.S. / Traynelis, S.F. / Egebjerg, J.
Citation
Journal: J.Biol.Chem. / Year: 2005
Title: A Binding Site Tyrosine Shapes Desensitization Kinetics and Agonist Potency at GluR2: a mutagenic, kinetic, and crystallographic study
Authors: Holm, M.M. / Naur, P. / Vestergaard, B. / Geballe, M.T. / Gajhede, M. / Kastrup, J.S. / Traynelis, S.F. / Egebjerg, J.
#1: 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.
#2: 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.
#3: Journal: Proc.Natl.Acad.Sci.USA / Year: 2003
Title: Tuning Activation of the Ampa-Sensitive Glur2 Ion Channel by Genetic Adjustment of Agonist-Induced
Authors: Armstrong, N. / Mayer, M. / Gouaux, E.
History
DepositionAug 11, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 30, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 2, 2017Group: Data collection / Refinement description / Source and taxonomy
Category: diffrn_source / entity_src_gen / software / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Oct 11, 2017Group: Refinement description / Category: software
Revision 1.5Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Remark 999SEQUENCE Native GluR2 is a membrane protein. The protein crystallized is the extracellular ligand ...SEQUENCE Native GluR2 is a membrane protein. The protein crystallized is the extracellular ligand binding domain of GluR2. Transmembrane regions were genetically removed and replaced with a Gly-Thr linker (residues 118-119).

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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)29,4582
Polymers29,2451
Non-polymers2131
Water4,504250
1
A: Glutamate receptor 2
hetero molecules

A: Glutamate receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,9164
Polymers58,4892
Non-polymers4262
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Unit cell
Length a, b, c (Å)95.254, 61.635, 48.751
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
DetailsThe intact receptor is a tetramer consisting of a dimer-of-dimers. Only the dimer can be found in the crystal by applying the following transformation to chain A: -1 0 0 0 -1 0 0 0 1 1 0 0

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Components

#1: Protein Glutamate receptor 2 / GluR-2 / GluR-B / GluR-K2 / Glutamate receptor ionotropic / AMPA 2


Mass: 29244.721 Da / Num. of mol.: 1 / Fragment: Ligand Binding Core / Mutation: Y61W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Gria2, Glur2 / 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-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.: 250 / 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: 2.47 Å3/Da / Density % sol: 50.15 %
Crystal growTemperature: 279 K / pH: 6.5
Details: PEG 8000, Cacodylate, Lithium Sulphate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 279K, pH 6.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 1.027
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 9, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.027 Å / Relative weight: 1
ReflectionResolution: 2.1→25 Å / Num. obs: 16201 / % possible obs: 92.9 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 17.15 Å2 / Rsym value: 0.107 / Net I/σ(I): 13.6
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 4.5 / Rsym value: 0.292 / % possible all: 94

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Phasing

Phasing MRRfactor: 51.9 / Cor.coef. Fo:Fc: 29.7 / Cor.coef. Io to Ic: 17.9
Highest resolutionLowest resolution
Rotation3 Å51.988 Å
Translation3 Å51.988 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
PDB_EXTRACT1.7data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1FTK

1ftk


Resolution: 2.1→25 Å / Rfactor Rfree error: 0.012 / Data cutoff high absF: 290292.49 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
Details: RESIDUE 263 COULD NOT BE MODELLED INTO THE ELECTRON DENSITY.
RfactorNum. reflection% reflectionSelection details
Rfree0.248 465 2.7 %RANDOM
Rwork0.187 ---
obs0.187 15598 89.9 %-
all-17355 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 43.37 Å2 / ksol: 0.370341 e/Å3
Displacement parametersBiso mean: 15.72 Å2
Baniso -1Baniso -2Baniso -3
1--0.104 Å20 Å20 Å2
2---0.926 Å20 Å2
3---1.03 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.18 Å0.1 Å
Refinement stepCycle: LAST / Resolution: 2.1→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2042 0 15 254 2311
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.77
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.034 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.288 73 2.9 %
Rwork0.194 2471 -
obs--89.6 %

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