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- PDB-3bfu: Structure of the ligand-binding core of GluR2 in complex with the... -

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Basic information

Entry
Database: PDB / ID: 3bfu
TitleStructure of the ligand-binding core of GluR2 in complex with the agonist (R)-TDPA at 1.95 A resolution
ComponentsGlutamate receptor 2
KeywordsMEMBRANE PROTEIN / AMPA receptor / GluR2 / ligand-binding core / agonist / (R)-TDPA / Alternative splicing / Cell junction / Endoplasmic reticulum / Glycoprotein / Ion transport / Ionic channel / Lipoprotein / Membrane / Palmitate / Phosphoprotein / Postsynaptic cell membrane / RNA editing / Synapse / Transmembrane / Transport
Function / homology
Function and homology information


spine synapse / dendritic spine neck / dendritic spine cytoplasm / dendritic spine head / cellular response to amine stimulus / perisynaptic space / Activation of AMPA receptors / ligand-gated monoatomic cation channel activity / AMPA glutamate receptor activity / response to lithium ion ...spine synapse / dendritic spine neck / dendritic spine cytoplasm / dendritic spine head / cellular response to amine stimulus / perisynaptic space / Activation of AMPA receptors / ligand-gated monoatomic cation channel activity / AMPA glutamate receptor activity / response to lithium ion / Trafficking of GluR2-containing AMPA receptors / AMPA glutamate receptor clustering / kainate selective glutamate receptor activity / cellular response to glycine / immunoglobulin binding / AMPA glutamate receptor complex / asymmetric synapse / extracellularly glutamate-gated ion channel activity / conditioned place preference / regulation of receptor recycling / ionotropic glutamate receptor complex / glutamate receptor binding / Unblocking of NMDA receptors, glutamate binding and activation / positive regulation of synaptic transmission / regulation of synaptic transmission, glutamatergic / response to fungicide / regulation of long-term synaptic depression / cytoskeletal protein binding / glutamate-gated receptor activity / extracellular ligand-gated monoatomic ion channel activity / cellular response to brain-derived neurotrophic factor stimulus / glutamate-gated calcium ion channel activity / presynaptic active zone membrane / somatodendritic compartment / dendrite membrane / ionotropic glutamate receptor binding / excitatory synapse / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / ionotropic glutamate receptor signaling pathway / dendrite cytoplasm / positive regulation of excitatory postsynaptic potential / synaptic membrane / dendritic shaft / SNARE binding / PDZ domain binding / synaptic transmission, glutamatergic / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / protein tetramerization / establishment of protein localization / cerebral cortex development / postsynaptic density membrane / modulation of chemical synaptic transmission / receptor internalization / Schaffer collateral - CA1 synapse / terminal bouton / synaptic vesicle / synaptic vesicle membrane / long-term synaptic potentiation / signaling receptor activity / presynapse / amyloid-beta binding / growth cone / presynaptic membrane / scaffold protein binding / perikaryon / dendritic spine / chemical synaptic transmission / postsynaptic membrane / neuron projection / postsynaptic density / axon / external side of plasma membrane / neuronal cell body / dendrite / synapse / protein kinase binding / protein-containing complex binding / glutamatergic synapse / cell surface / endoplasmic reticulum / protein-containing complex / identical protein binding / membrane / plasma membrane
Similarity search - Function
Ionotropic glutamate receptor, metazoa / Ligated ion channel L-glutamate- and glycine-binding site / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / Ligated ion channel L-glutamate- and glycine-binding site / Ligand-gated ion channel / : / Ionotropic glutamate receptor / Eukaryotic homologues of bacterial periplasmic substrate binding proteins. / Receptor, ligand binding region / Receptor family ligand binding region ...Ionotropic glutamate receptor, metazoa / Ligated ion channel L-glutamate- and glycine-binding site / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / Ligated ion channel L-glutamate- and glycine-binding site / Ligand-gated ion channel / : / 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-R2P / Glutamate receptor 2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.95 Å
AuthorsBeich-Frandsen, M. / Mirza, O. / Vestergaard, B. / Gajhede, M. / Kastrup, J.S.
Citation
Journal: J.Med.Chem. / Year: 2008
Title: Structures of the ligand-binding core of iGluR2 in complex with the agonists (R)- and (S)-2-amino-3-(4-hydroxy-1,2,5-thiadiazol-3-yl)propionic acid explain their unusual equipotency.
Authors: Beich-Frandsen, M. / Pickering, D.S. / Mirza, O. / Johansen, T.N. / Greenwood, J. / Vestergaard, B. / Schousboe, A. / Gajhede, M. / Liljefors, T. / Kastrup, J.S.
#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.
History
DepositionNov 23, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 14, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 23, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.3Oct 25, 2017Group: Refinement description / Category: software
Revision 1.4Nov 1, 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 / 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 / _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 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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
D: Glutamate receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,6438
Polymers116,8874
Non-polymers7574
Water21,9421218
1
A: Glutamate receptor 2
hetero molecules

A: Glutamate receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,8224
Polymers58,4432
Non-polymers3782
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area1840 Å2
MethodPISA
2
B: Glutamate receptor 2
hetero molecules

B: Glutamate receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,8224
Polymers58,4432
Non-polymers3782
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area1700 Å2
MethodPISA
3
C: Glutamate receptor 2
hetero molecules

C: Glutamate receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,8224
Polymers58,4432
Non-polymers3782
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area1810 Å2
MethodPISA
4
D: Glutamate receptor 2
hetero molecules

D: Glutamate receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,8224
Polymers58,4432
Non-polymers3782
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area1770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.750, 47.520, 124.330
Angle α, β, γ (deg.)90.000, 113.540, 90.000
Int Tables number3
Space group name H-MP121

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Components

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


Mass: 29221.682 Da / Num. of mol.: 4 / Fragment: residues 1-263
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Gria2, Glur2 / Plasmid: PETGQ KANR / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P19491
#2: Chemical
ChemComp-R2P / (2R)-2-amino-3-(4-hydroxy-1,2,5-thiadiazol-3-yl)propanoic acid


Type: D-peptide linking / Mass: 189.192 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5H7N3O3S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1218 / 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: 2.43 Å3/Da / Density % sol: 49.32 %
Crystal growTemperature: 279 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 2000, cacodylate, ammonium sulfate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 279K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.8122 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jun 27, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8122 Å / Relative weight: 1
ReflectionResolution: 1.95→96.23 Å / Num. obs: 82554 / % possible obs: 99.9 % / Redundancy: 5.2 % / Rsym value: 0.133 / Net I/σ(I): 10.8
Reflection shellResolution: 1.95→2.06 Å / Redundancy: 5.1 % / Mean I/σ(I) obs: 3.6 / Num. unique all: 11970 / Rsym value: 0.506 / % possible all: 99.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
MOLREPphasing
CNS1.1refinement
PDB_EXTRACT3.004data extraction
xia2data scaling
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1MQD

1mqd


Resolution: 1.95→96.23 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.233 4167 5 %Random
Rwork0.2 ---
obs-82548 99.9 %-
Solvent computationBsol: 44.573 Å2
Displacement parametersBiso mean: 18.624 Å2
Baniso -1Baniso -2Baniso -3
1--1.589 Å20 Å2-2.382 Å2
2--2.976 Å20 Å2
3----1.387 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.21 Å0.15 Å
Refinement stepCycle: LAST / Resolution: 1.95→96.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8139 0 48 1218 9405
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_mcbond_it1.2641.5
X-RAY DIFFRACTIONc_scbond_it2.162
X-RAY DIFFRACTIONc_mcangle_it1.8712
X-RAY DIFFRACTIONc_scangle_it3.1442.5
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5lig.paramlig.top

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