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- PDB-3bki: Crystal Structure of the GluR2 ligand binding core (S1S2J) in com... -

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Basic information

Entry
Database: PDB / ID: 3bki
TitleCrystal Structure of the GluR2 ligand binding core (S1S2J) in complex with FQX at 1.87 Angstroms
ComponentsGlutamate receptor 2
KeywordsTRANSPORT PROTEIN / AMPA receptor / ANQX / quinoxaline-2 / 3-diones / 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 head / Activation of AMPA receptors / perisynaptic space / AMPA glutamate receptor activity / ligand-gated monoatomic cation channel activity / Trafficking of GluR2-containing AMPA receptors / response to lithium ion / immunoglobulin binding ...spine synapse / dendritic spine neck / dendritic spine head / Activation of AMPA receptors / perisynaptic space / AMPA glutamate receptor activity / ligand-gated monoatomic cation channel 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 / cellular response to glycine / extracellularly glutamate-gated ion channel activity / asymmetric synapse / regulation of receptor recycling / Unblocking of NMDA receptors, glutamate binding and activation / positive regulation of synaptic transmission / glutamate receptor binding / glutamate-gated receptor activity / regulation of synaptic transmission, glutamatergic / response to fungicide / cytoskeletal protein binding / ionotropic glutamate receptor binding / presynaptic active zone membrane / extracellular ligand-gated monoatomic ion channel activity / somatodendritic compartment / glutamate-gated calcium ion channel activity / cellular response to brain-derived neurotrophic factor stimulus / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / dendrite membrane / dendrite cytoplasm / ionotropic glutamate receptor signaling pathway / SNARE binding / dendritic shaft / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / synaptic transmission, glutamatergic / PDZ domain binding / protein tetramerization / establishment of protein localization / synaptic membrane / modulation of chemical synaptic transmission / postsynaptic density membrane / terminal bouton / Schaffer collateral - CA1 synapse / cerebral cortex development / receptor internalization / synaptic vesicle membrane / synaptic vesicle / presynapse / signaling receptor activity / amyloid-beta binding / presynaptic membrane / growth cone / scaffold protein binding / chemical synaptic transmission / dendritic spine / perikaryon / postsynaptic membrane / neuron projection / postsynaptic density / axon / neuronal cell body / synapse / dendrite / protein-containing complex binding / protein kinase 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-FQX / Glutamate receptor 2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.87 Å
AuthorsCruz, L. / Estebanez-Perpina, E. / Pfaff, S. / Borngraeber, S. / Bao, N. / Fletterick, R. / England, P.
CitationJournal: J.Med.Chem. / Year: 2008
Title: 6-Azido-7-nitro-1,4-dihydroquinoxaline-2,3-dione (ANQX) forms an irreversible bond to the active site of the GluR2 AMPA receptor.
Authors: Cruz, L.A. / Estebanez-Perpina, E. / Pfaff, S. / Borngraeber, S. / Bao, N. / Blethrow, J. / Fletterick, R.J. / England, P.M.
History
DepositionDec 6, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 16, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 2, 2017Group: Data collection / Refinement description / Source and taxonomy
Category: entity_src_gen / reflns / software / Item: _reflns.percent_possible_obs
Revision 1.3Sep 4, 2019Group: Data collection / Category: reflns / reflns_shell
Item: _reflns.observed_criterion_sigma_F / _reflns.observed_criterion_sigma_I ..._reflns.observed_criterion_sigma_F / _reflns.observed_criterion_sigma_I / _reflns.pdbx_Rmerge_I_obs / _reflns.pdbx_Rsym_value / _reflns.pdbx_netI_over_sigmaI / _reflns.pdbx_redundancy / _reflns.percent_possible_obs / _reflns_shell.Rmerge_I_obs / _reflns_shell.meanI_over_sigI_obs / _reflns_shell.percent_possible_all
Revision 1.4Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
P: Glutamate receptor 2
B: Glutamate receptor 2
C: Glutamate receptor 2
D: Glutamate receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,7678
Polymers116,8874
Non-polymers8814
Water15,403855
1
P: Glutamate receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,4422
Polymers29,2221
Non-polymers2201
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Glutamate receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,4422
Polymers29,2221
Non-polymers2201
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Glutamate receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,4422
Polymers29,2221
Non-polymers2201
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Glutamate receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,4422
Polymers29,2221
Non-polymers2201
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)62.340, 92.260, 195.240
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Gria2, Glur2 / Production host: Escherichia coli (E. coli) / References: UniProt: P19491
#2: Chemical
ChemComp-FQX / [1,2,5]oxadiazolo[3,4-g]quinoxaline-6,7(5H,8H)-dione 1-oxide


Mass: 220.142 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H4N4O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 855 / 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

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Sample preparation

CrystalDensity Matthews: 2.4 Å3/Da / Density % sol: 48.79 %
Crystal growMethod: vapor diffusion, hanging drop / Details: VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.7→25 Å / Num. obs: 114474 / % possible obs: 97 % / Redundancy: 2.1 % / Biso Wilson estimate: 12.3 Å2 / Rmerge(I) obs: 0.056 / Net I/σ(I): 8
Reflection shellResolution: 1.7→1.75 Å / Rmerge(I) obs: 0.512 / Mean I/σ(I) obs: 2 / % possible all: 92.8

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Processing

Software
NameClassification
HKL-2000data collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.87→19.98 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 2796927.14 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.221 4527 5 %RANDOM
Rwork0.213 ---
obs0.213 89972 95.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 46.61 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 18.4 Å2
Baniso -1Baniso -2Baniso -3
1--3.61 Å20 Å20 Å2
2--3.99 Å20 Å2
3----0.38 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.24 Å0.27 Å
Refinement stepCycle: LAST / Resolution: 1.87→19.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8036 0 64 855 8955
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.017
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_deg1.7
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.1
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: 1.87→1.99 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.311 668 4.8 %
Rwork0.317 13198 -
obs--89.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4FUROXAN.PARFUROXAN.TOP

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