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- PDB-4f2q: Quisqualate bound to the D655A mutant of the ligand binding domai... -

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Basic information

Entry
Database: PDB / ID: 4f2q
TitleQuisqualate bound to the D655A mutant of the ligand binding domain of GluA3
ComponentsGlutamate receptor 3
KeywordsTRANSPORT PROTEIN/AGONIST / glutamate receptor / GluA3 / GluR3 / AMPA receptor / S1S2 / LBD / neurotransmitter receptor / quisqualate / TRANSPORT PROTEIN-AGONIST complex
Function / homology
Function and homology information


Trafficking of AMPA receptors / Synaptic adhesion-like molecules / protein heterotetramerization / Activation of AMPA receptors / parallel fiber to Purkinje cell synapse / AMPA glutamate receptor activity / response to lithium ion / Trafficking of GluR2-containing AMPA receptors / AMPA glutamate receptor complex / asymmetric synapse ...Trafficking of AMPA receptors / Synaptic adhesion-like molecules / protein heterotetramerization / Activation of AMPA receptors / parallel fiber to Purkinje cell synapse / AMPA glutamate receptor activity / response to lithium ion / Trafficking of GluR2-containing AMPA receptors / AMPA glutamate receptor complex / asymmetric synapse / ionotropic glutamate receptor complex / regulation of receptor recycling / Unblocking of NMDA receptors, glutamate binding and activation / synaptic cleft / response to fungicide / glutamate-gated receptor activity / glutamate-gated calcium ion channel activity / presynaptic active zone membrane / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / dendritic shaft / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / synaptic transmission, glutamatergic / postsynaptic density membrane / modulation of chemical synaptic transmission / long-term synaptic potentiation / terminal bouton / amyloid-beta binding / presynaptic membrane / perikaryon / protein homotetramerization / dendritic spine / postsynaptic membrane / postsynaptic density / neuronal cell body / dendrite / glutamatergic synapse / protein-containing complex / 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-QUS / Glutamate receptor 3
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.202 Å
AuthorsAhmed, A.H. / Oswald, R.E.
CitationJournal: Biochemistry / Year: 2012
Title: The loss of an electrostatic contact unique to AMPA receptor ligand binding domain 2 slows channel activation.
Authors: Holley, S.M. / Ahmed, A.H. / Srinivasan, J. / Murthy, S.E. / Weiland, G.A. / Oswald, R.E. / Nowak, L.M.
History
DepositionMay 8, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 30, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 20, 2012Group: Database references
Revision 1.2Aug 16, 2017Group: Data collection / Source and taxonomy / Category: diffrn_detector / entity_src_gen / Item: _diffrn_detector.detector
Revision 1.3Sep 13, 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 1.4Nov 6, 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 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1813
Polymers28,9261
Non-polymers2552
Water3,351186
1
A: Glutamate receptor 3
hetero molecules

A: Glutamate receptor 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,3626
Polymers57,8532
Non-polymers5094
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area2580 Å2
ΔGint-64 kcal/mol
Surface area23800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.660, 48.027, 136.861
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number17
Space group name H-MP2221

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Components

#1: Protein Glutamate receptor 3 / GluR-3 / AMPA-selective glutamate receptor 3 / GluR-C / GluR-K3 / Glutamate receptor ionotropic / ...GluR-3 / AMPA-selective glutamate receptor 3 / GluR-C / GluR-K3 / Glutamate receptor ionotropic / AMPA 3 / GluA3


Mass: 28926.391 Da / Num. of mol.: 1 / Mutation: D655A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Glur3, Gria3, Gria3; GluA3 / Plasmid: pET-22b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): Origami B (DE3) / References: UniProt: P19492
#2: Chemical ChemComp-QUS / (S)-2-AMINO-3-(3,5-DIOXO-[1,2,4]OXADIAZOLIDIN-2-YL)-PROPIONIC ACID / QUISQUALATE


Mass: 189.126 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H7N3O5
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 186 / 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: 2.71 Å3/Da / Density % sol: 54.57 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 14-15% PEG 8K, 0.1 M sodium cacodylate, 0.1-0.15 M zinc acetate, 0.25 M ammonium sulfate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.977 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 13, 2009
RadiationMonochromator: Rh coated Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.5 % / Rmerge(I) obs: 0.189 / Rsym value: 0.189 / Net I/σ(I): 10.406
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.758 / Mean I/σ(I) obs: 2.194 / Rsym value: 0.758 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-3000data collection
PHENIXmodel building
PHENIX(phenix.refine)refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3DLN

3dln


Resolution: 2.202→22.659 Å / SU ML: 0.3 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0.08 / Phase error: 25.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2609 1553 10.03 %RANDOM
Rwork0.1946 ---
all0.2279 16592 --
obs0.2014 15490 93.36 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 33.584 Å2 / ksol: 0.338 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--7.7468 Å20 Å2-0 Å2
2--5.7775 Å20 Å2
3----1.8013 Å2
Refinement stepCycle: LAST / Resolution: 2.202→22.659 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2029 0 14 186 2229
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0132078
X-RAY DIFFRACTIONf_angle_d1.4662796
X-RAY DIFFRACTIONf_dihedral_angle_d16.896780
X-RAY DIFFRACTIONf_chiral_restr0.088307
X-RAY DIFFRACTIONf_plane_restr0.008348
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.202-2.27270.31451300.22451132X-RAY DIFFRACTION85
2.2727-2.35380.30621270.21661166X-RAY DIFFRACTION89
2.3538-2.44790.3321280.21561207X-RAY DIFFRACTION90
2.4479-2.55920.32111340.22421218X-RAY DIFFRACTION91
2.5592-2.69390.29161440.21951277X-RAY DIFFRACTION95
2.6939-2.86240.26881360.22291266X-RAY DIFFRACTION95
2.8624-3.08290.2871450.21021294X-RAY DIFFRACTION96
3.0829-3.39220.25681520.19351317X-RAY DIFFRACTION97
3.3922-3.8810.25091460.17531319X-RAY DIFFRACTION98
3.881-4.88160.20861490.15161365X-RAY DIFFRACTION97
4.8816-22.660.22471620.18991376X-RAY DIFFRACTION94

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