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- PDB-4u23: GluA2flip sLBD complexed with FW and (R,R)-2b crystal form F -

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Basic information

Entry
Database: PDB / ID: 4u23
TitleGluA2flip sLBD complexed with FW and (R,R)-2b crystal form F
ComponentsGlutamate receptor 2,Glutamate receptor 2
KeywordsTransport Protein / Membrane Protein / AMPA receptor
Function / homology
Function and homology information


spine synapse / dendritic spine neck / 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 ...spine synapse / dendritic spine neck / 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 / kainate selective glutamate receptor activity / cellular response to glycine / AMPA glutamate receptor complex / extracellularly glutamate-gated ion channel activity / immunoglobulin binding / asymmetric synapse / ionotropic glutamate receptor complex / conditioned place preference / regulation of receptor recycling / glutamate receptor binding / Unblocking of NMDA receptors, glutamate binding and activation / positive regulation of synaptic transmission / regulation of synaptic transmission, glutamatergic / response to fungicide / cytoskeletal protein binding / glutamate-gated receptor activity / regulation of long-term synaptic depression / 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 / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / ionotropic glutamate receptor signaling pathway / dendrite cytoplasm / synaptic membrane / dendritic shaft / SNARE binding / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / synaptic transmission, glutamatergic / protein tetramerization / PDZ domain binding / establishment of protein localization / postsynaptic density membrane / cerebral cortex development / modulation of chemical synaptic transmission / receptor internalization / Schaffer collateral - CA1 synapse / terminal bouton / synaptic vesicle / synaptic vesicle membrane / presynapse / signaling receptor activity / amyloid-beta binding / presynaptic membrane / growth cone / scaffold protein binding / perikaryon / chemical synaptic transmission / dendritic spine / 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-FWD / Chem-FWF / Glutamate receptor 2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.6734 Å
AuthorsChen, L. / Gouaux, E.
CitationJournal: Cell / Year: 2014
Title: Structure and Dynamics of AMPA Receptor GluA2 in Resting, Pre-Open, and Desensitized States.
Authors: Durr, K.L. / Chen, L. / Stein, R.A. / De Zorzi, R. / Folea, I.M. / Walz, T. / Mchaourab, H.S. / Gouaux, E.
History
DepositionJul 16, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 20, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 1, 2014Group: Database references
Revision 1.2Dec 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_src_gen / pdbx_database_status / pdbx_struct_oper_list / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_oper_list.symmetry_operation / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein
Revision 1.3Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)29,8923
Polymers29,1941
Non-polymers6982
Water3,873215
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.090, 91.290, 111.940
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Glutamate receptor 2,Glutamate receptor 2 / GluR-2 / AMPA-selective glutamate receptor 2 / GluR-B / GluR-K2 / Glutamate receptor ionotropic / ...GluR-2 / AMPA-selective glutamate receptor 2 / GluR-B / GluR-K2 / Glutamate receptor ionotropic / AMPA 2 / GluA2


Mass: 29193.670 Da / Num. of mol.: 1 / Mutation: A796S
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-FWD / 2-AMINO-3-(5-FLUORO-2,4-DIOXO-3,4-DIHYDRO-2H-PYRIMIDIN-1-YL)-PROPIONIC ACID / FLUORO-WILLARDIINE


Mass: 217.155 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H8FN3O4
#3: Chemical ChemComp-FWF / N,N'-[biphenyl-4,4'-diyldi(2R)propane-2,1-diyl]dipropane-2-sulfonamide


Mass: 480.684 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H36N2O4S2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 215 / 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: 2.63 Å3/Da / Density % sol: 53.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M bicine/Trizma base, pH 8.5, 0.09 M Morpheus nitrate-phosphate-sulfate, 10% w/v PEG8K, 20% (v/v) ethylene glycol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 2, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.67→42.27 Å / Num. obs: 35750 / % possible obs: 99.6 % / Redundancy: 4 % / Biso Wilson estimate: 24.3 Å2 / Net I/σ(I): 22

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Processing

Software
NameVersionClassification
XDSdata reduction
PDB_EXTRACT3.14data extraction
PHENIX(phenix.refine: 1.8.2_1309)refinement
RefinementResolution: 1.6734→42.266 Å / FOM work R set: 0.7401 / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2499 1789 5.01 %
Rwork0.2182 33929 -
obs0.2198 35718 99.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 75.25 Å2 / Biso mean: 24.82 Å2 / Biso min: 6.13 Å2
Refinement stepCycle: final / Resolution: 1.6734→42.266 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2010 0 47 215 2272
Biso mean--13.11 31.67 -
Num. residues----259
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062096
X-RAY DIFFRACTIONf_angle_d1.062825
X-RAY DIFFRACTIONf_chiral_restr0.07314
X-RAY DIFFRACTIONf_plane_restr0.005348
X-RAY DIFFRACTIONf_dihedral_angle_d12.744781
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6734-1.71870.39311440.35032579272399
1.7187-1.76920.33261390.32325572696100
1.7692-1.82630.34181230.29412591271499
1.8263-1.89160.33551330.27862585271899
1.8916-1.96730.2941200.257125842704100
1.9673-2.05690.29121430.244925842727100
2.0569-2.16530.3061420.243925932735100
2.1653-2.3010.25231410.243226082749100
2.301-2.47860.28771340.234626202754100
2.4786-2.7280.2411370.229126242761100
2.728-3.12260.28181330.226526132746100
3.1226-3.93380.24071510.19312648279999
3.9338-42.27970.18191490.17342743289299

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