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- PDB-3bbr: Crystal structure of the iGluR2 ligand binding core (S1S2J-N775S)... -

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Basic information

Entry
Database: PDB / ID: 3bbr
TitleCrystal structure of the iGluR2 ligand binding core (S1S2J-N775S) in complex with a dimeric positive modulator as well as glutamate at 2.25 A resolution
ComponentsGlutamate receptor 2
KeywordsMEMBRANE PROTEIN / AMPA RECEPTOR / GLUR2 / S1S2 / LIGAND BINDING CORE / POINT MUTATION / N775S / DIMERIC POSITIVE MODULATOR / AGONIST / Cell junction / Glycoprotein / Ion transport / Ionic channel / Lipoprotein / Membrane / Palmitate / Phosphorylation / Postsynaptic cell membrane / RNA editing / Synapse / Transmembrane / Transport
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
Chem-BHY / GLUTAMIC ACID / Glutamate receptor 2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.25 Å
AuthorsKastrup, J.S. / Gajhede, M.
CitationJournal: Chem.Biol. / Year: 2007
Title: Structural proof of a dimeric positive modulator bridging two identical AMPA receptor-binding sites
Authors: Kaae, B.H. / Harpsoe, K. / Kastrup, J.S. / Sanz, A.C. / Pickering, D.S. / Metzler, B. / Clausen, R.P. / Gajhede, M. / Sauerberg, P. / Liljefors, T. / Madsen, U.
History
DepositionNov 11, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 4, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Aug 16, 2017Group: Data collection / Refinement description / Source and taxonomy
Category: diffrn_source / entity_src_gen / software / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Nov 10, 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 1.4Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glutamate receptor 2
B: Glutamate receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,80813
Polymers58,3892
Non-polymers1,41911
Water9,440524
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3340 Å2
ΔGint-79 kcal/mol
Surface area24000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.080, 121.780, 47.427
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 29194.658 Da / Num. of mol.: 2 / Fragment: Ligand binding core / Mutation: N775S
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

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Non-polymers , 6 types, 535 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-GLU / GLUTAMIC ACID


Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H9NO4
#5: Chemical ChemComp-BHY / N,N'-[biphenyl-4,4'-diyldi(2R)propane-2,1-diyl]dimethanesulfonamide / (R,R)-N,N-(2,2'-(biphenyl-4-4'-diyl)bis(propane-2,1-diyl))dimethanesulfonamide


Mass: 424.577 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H28N2O4S2
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 524 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsTHE NATIVE GLUR2 IS A MEMBRANE PROTEIN. TRANSMEMBRANE REGIONS WERE GENETICALLY REMOVED AND REPLACED ...THE NATIVE GLUR2 IS A MEMBRANE PROTEIN. TRANSMEMBRANE REGIONS WERE GENETICALLY REMOVED AND REPLACED WITH A GLY-THR LINKER.

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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: 2.45 Å3/Da / Density % sol: 49.8 %
Crystal growTemperature: 280 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.3M ammonium sulfate, 0.1M sodium acetate, 25% PEG 4000, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 280K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-2 / Wavelength: 1.043
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Mar 13, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.043 Å / Relative weight: 1
ReflectionResolution: 2.25→122.169 Å / Num. obs: 27875 / % possible obs: 99.6 % / Redundancy: 6.3 % / Biso Wilson estimate: 16 Å2 / Rmerge(I) obs: 0.09 / Rsym value: 0.09 / Net I/σ(I): 6.7
Reflection shellResolution: 2.25→2.37 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.263 / Mean I/σ(I) obs: 2.3 / Num. measured all: 25558 / Num. unique all: 3992 / Rsym value: 0.263 / % possible all: 99.4

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALAdata scaling
PHENIXrefinement
PDB_EXTRACT3.004data extraction
RefinementStarting model: 1LB8

1lb8


Resolution: 2.25→38.428 Å / Num. restraintsaints: 57427 / FOM work R set: 0.829 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.231 1394 5.01 %Random
Rwork0.169 ---
obs-27839 99.4 %-
Solvent computationBsol: 50.056 Å2 / ksol: 0.34 e/Å3
Displacement parametersBiso max: 34.51 Å2 / Biso mean: 11.5 Å2 / Biso min: 2.3 Å2
Baniso -1Baniso -2Baniso -3
1-9 Å20 Å20 Å2
2--5.305 Å20 Å2
3---5.459 Å2
Refinement stepCycle: LAST / Resolution: 2.25→38.428 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4046 0 86 524 4656
Refine LS restraints
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONf_angle_d0.6981
X-RAY DIFFRACTIONf_bond_d0.0051
X-RAY DIFFRACTIONf_chiral_restr0.0491
X-RAY DIFFRACTIONf_dihedral_angle_d10.3571
X-RAY DIFFRACTIONf_plane_restr0.0031
X-RAY DIFFRACTIONf_nbd_refined4.0721

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