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- PDB-4f2o: Quisqualate bound to the D655A mutant of the ligand binding domai... -

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Basic information

Entry
Database: PDB / ID: 4f2o
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 / parallel fiber to Purkinje cell synapse / Activation of AMPA receptors / 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 / parallel fiber to Purkinje cell synapse / Activation of AMPA receptors / 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: 1.912 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 23, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 16, 2017Group: Data collection / Source and taxonomy / Category: diffrn_detector / entity_src_gen / Item: _diffrn_detector.detector
Revision 1.2Sep 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 1.3Nov 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
Water6,305350
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 area2690 Å2
ΔGint-64 kcal/mol
Surface area23730 Å2
MethodPISA
2
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 operation3_554-x,y,-z-1/21
Buried area1470 Å2
ΔGint-80 kcal/mol
Surface area24950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.594, 47.825, 136.555
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number17
Space group name H-MP2221
Components on special symmetry positions
IDModelComponents
11A-561-

HOH

21A-573-

HOH

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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.: 350 / 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: 2.69 Å3/Da / Density % sol: 54.21 %
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: 1.9→50 Å / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.4 % / Rmerge(I) obs: 0.085 / Rsym value: 0.085 / Net I/σ(I): 19.646
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.436 / Mean I/σ(I) obs: 2.93 / Rsym value: 0.436 / % possible all: 99.9

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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: 1.912→21.089 Å / SU ML: 0.27 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0.09 / Phase error: 22.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2279 1924 8.09 %RANDOM
Rwork0.1883 ---
all0.1916 24892 --
obs0.1916 23777 95.52 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 57.484 Å2 / ksol: 0.365 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.3439 Å20 Å20 Å2
2--3.1041 Å2-0 Å2
3----0.7602 Å2
Refinement stepCycle: LAST / Resolution: 1.912→21.089 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2026 0 14 350 2390
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082075
X-RAY DIFFRACTIONf_angle_d1.1482794
X-RAY DIFFRACTIONf_dihedral_angle_d16.651777
X-RAY DIFFRACTIONf_chiral_restr0.08307
X-RAY DIFFRACTIONf_plane_restr0.009349
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.912-1.95960.28311110.20691272X-RAY DIFFRACTION80
1.9596-2.01250.24881280.19091500X-RAY DIFFRACTION93
2.0125-2.07170.26581250.1771522X-RAY DIFFRACTION94
2.0717-2.13850.25581290.16931512X-RAY DIFFRACTION94
2.1385-2.21480.24141400.17751546X-RAY DIFFRACTION96
2.2148-2.30340.23621400.17641561X-RAY DIFFRACTION97
2.3034-2.40810.24751410.18231583X-RAY DIFFRACTION97
2.4081-2.53490.27521430.18821574X-RAY DIFFRACTION98
2.5349-2.69340.23921380.1891590X-RAY DIFFRACTION98
2.6934-2.90090.22921430.19591594X-RAY DIFFRACTION98
2.9009-3.19190.23891440.18821631X-RAY DIFFRACTION99
3.1919-3.65170.20421490.16961615X-RAY DIFFRACTION98
3.6517-4.59290.17431400.16651645X-RAY DIFFRACTION98
4.5929-21.09010.21411530.22111708X-RAY DIFFRACTION96

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