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- PDB-1lbb: Crystal structure of the GluR2 ligand binding domain mutant (S1S2... -

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Basic information

Entry
Database: PDB / ID: 1lbb
TitleCrystal structure of the GluR2 ligand binding domain mutant (S1S2J-N754D) in complex with kainate at 2.1 A resolution
ComponentsGlutamine receptor 2
KeywordsMEMBRANE PROTEIN / AMPA receptor / GluR2 / S1S2 / Ligand-binding core / Point mutation / N754D / Agonist / Kainate
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 / presynaptic active zone membrane / glutamate-gated receptor activity / 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 / cytoskeletal protein binding / dendrite cytoplasm / SNARE binding / dendritic shaft / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / synaptic membrane / synaptic transmission, glutamatergic / PDZ domain binding / postsynaptic density membrane / protein tetramerization / 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 / perikaryon / scaffold protein binding / chemical synaptic transmission / postsynaptic membrane / dendritic spine / postsynaptic density / neuron projection / axon / neuronal cell body / synapse / glutamatergic synapse / dendrite / 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
3-(CARBOXYMETHYL)-4-ISOPROPENYLPROLINE / Glutamate receptor 2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsSun, Y. / Olson, R. / Horning, M. / Armstrong, N. / Mayer, M. / Gouaux, E.
CitationJournal: Nature / Year: 2002
Title: Mechanism of glutamate receptor desensitization.
Authors: Sun, Y. / Olson, R. / Horning, M. / Armstrong, N. / Mayer, M. / Gouaux, E.
History
DepositionApr 2, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 5, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.4Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / struct_ref_seq_dif ...database_2 / struct_ref_seq_dif / struct_sheet / 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_sheet.number_strands / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999Sequence The native GLUR-2 is a membrane protein. The protein crystallized by the author is the ...Sequence The native GLUR-2 is a membrane protein. The protein crystallized by the author is the extracellular ligand binding domain of GLUR-2. Transmembrane regions were genetically removed and replaced with a Gly-Thr linker. The sequence, as a result, matches discontinuously with the reference database.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glutamine receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,4362
Polymers29,2231
Non-polymers2131
Water2,522140
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.990, 63.270, 46.510
Angle α, β, γ (deg.)90.00, 92.25, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Glutamine receptor 2 / GLUR-2 / GLUR-B / GLUR-K2 / GLUTAMATE RECEPTOR IONOTROPIC AMPA 2


Mass: 29222.670 Da / Num. of mol.: 1 / Fragment: ligand binding core (flop) / Mutation: N754D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: GluR-2 / 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 / Kainic acid


Mass: 213.230 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15NO4 / Comment: neurotransmitter, agonist*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 140 / 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: 2.21 Å3/Da / Density % sol: 44.41 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 1000, Li2SO4, phosphate-citrate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jul 1, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→20 Å / Num. all: 13044 / Num. obs: 13044 / % possible obs: 87.1 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 12.7 Å2
Reflection shellResolution: 2.1→2.18 Å / % possible all: 91

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→20 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 890900.72 / Data cutoff high rms absF: 890900.72 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.26 1321 10.3 %RANDOM
Rwork0.201 ---
all-12800 --
obs-12800 85.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 43.4362 Å2 / ksol: 0.342414 e/Å3
Displacement parametersBiso mean: 20.4 Å2
Baniso -1Baniso -2Baniso -3
1-2.03 Å20 Å20.99 Å2
2---0.84 Å20 Å2
3----1.19 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.2 Å0.11 Å
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1972 0 15 140 2127
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d21.7
X-RAY DIFFRACTIONc_improper_angle_d0.97
X-RAY DIFFRACTIONc_mcbond_it1.261.5
X-RAY DIFFRACTIONc_mcangle_it1.912
X-RAY DIFFRACTIONc_scbond_it2.082
X-RAY DIFFRACTIONc_scangle_it2.92.5
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.294 232 10.8 %
Rwork0.213 1912 -
obs--86.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3KAI.PARKAI.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP

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