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- PDB-4f1y: CNQX bound to the ligand binding domain of GluA3 -

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Basic information

Entry
Database: PDB / ID: 4f1y
TitleCNQX bound to the ligand binding domain of GluA3
ComponentsGlutamate receptor 3
KeywordsTRANSPORT PROTEIN/AGONIST / glutamate receptor / GluA3 / GluR3 / AMPA receptor / S1S2 / LBD / neurotransmitter receptor / CNQX / TRANSPORT PROTEIN / TRANSPORT PROTEIN-AGONIST complex
Function / homology
Function and homology information


chemical synaptic transmission, postsynaptic / Trafficking of AMPA receptors / Synaptic adhesion-like molecules / parallel fiber to Purkinje cell synapse / Activation of AMPA receptors / response to lithium ion / AMPA glutamate receptor activity / Trafficking of GluR2-containing AMPA receptors / AMPA glutamate receptor complex / ionotropic glutamate receptor complex ...chemical synaptic transmission, postsynaptic / Trafficking of AMPA receptors / Synaptic adhesion-like molecules / parallel fiber to Purkinje cell synapse / Activation of AMPA receptors / response to lithium ion / AMPA glutamate receptor activity / Trafficking of GluR2-containing AMPA receptors / AMPA glutamate receptor complex / ionotropic glutamate receptor complex / asymmetric synapse / regulation of receptor recycling / Unblocking of NMDA receptors, glutamate binding and activation / regulation of postsynaptic membrane potential / glutamate-gated receptor activity / synaptic cleft / presynaptic active zone membrane / response to fungicide / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / monoatomic ion transmembrane transport / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / dendritic shaft / synaptic transmission, glutamatergic / postsynaptic density membrane / modulation of chemical synaptic transmission / terminal bouton / presynaptic membrane / amyloid-beta binding / perikaryon / chemical synaptic transmission / postsynaptic membrane / dendritic spine / postsynaptic density / neuronal cell body / dendrite / glutamatergic synapse / protein-containing complex / membrane / 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
Chem-CNI / Glutamate receptor 3
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.79 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 7, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 16, 2012Provider: repository / Type: Initial release
Revision 1.1May 23, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glutamate receptor 3
C: Glutamate receptor 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,5326
Polymers57,9412
Non-polymers5914
Water8,863492
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1910 Å2
ΔGint-65 kcal/mol
Surface area24510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.183, 96.846, 62.229
Angle α, β, γ (deg.)90.00, 107.15, 90.00
Int Tables number4
Space group name H-MP1211

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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: 28970.402 Da / Num. of mol.: 2
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-CNI / 7-nitro-2,3-dioxo-2,3-dihydroquinoxaline-6-carbonitrile


Mass: 230.137 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H2N4O4
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 492 / 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: 2.49 Å3/Da / Density % sol: 50.68 %
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: Mar 14, 2010
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: 1.79→50 Å / % possible obs: 95.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 2.9 % / Rmerge(I) obs: 0.087 / Rsym value: 0.087 / Net I/σ(I): 23.26
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.489 / Mean I/σ(I) obs: 2.059 / Rsym value: 0.489 / % possible all: 98.2

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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: 3B7D

3b7d


Resolution: 1.79→26.779 Å / SU ML: 0.27 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0.05 / Phase error: 26.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2508 1862 3.92 %RANDOM
Rwork0.2057 ---
all0.2075 53414 --
obs0.2075 47533 88.99 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.983 Å2 / ksol: 0.378 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-16.297 Å2-0 Å2-0.4422 Å2
2---8.5661 Å20 Å2
3----7.7309 Å2
Refinement stepCycle: LAST / Resolution: 1.79→26.779 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4051 0 36 492 4579
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064169
X-RAY DIFFRACTIONf_angle_d1.0365617
X-RAY DIFFRACTIONf_dihedral_angle_d16.4221543
X-RAY DIFFRACTIONf_chiral_restr0.072617
X-RAY DIFFRACTIONf_plane_restr0.005700
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.79-1.83880.25771070.24222665X-RAY DIFFRACTION68
1.8388-1.89290.29181330.21133255X-RAY DIFFRACTION83
1.8929-1.9540.24351330.19823416X-RAY DIFFRACTION87
1.954-2.02380.24941430.19023549X-RAY DIFFRACTION90
2.0238-2.10480.24881510.19653679X-RAY DIFFRACTION93
2.1048-2.20060.21781500.19583679X-RAY DIFFRACTION94
2.2006-2.31650.2621510.1883732X-RAY DIFFRACTION94
2.3165-2.46160.2051550.19613722X-RAY DIFFRACTION95
2.4616-2.65150.24291530.20273743X-RAY DIFFRACTION95
2.6515-2.9180.2561550.21223746X-RAY DIFFRACTION95
2.918-3.33960.27271530.21263728X-RAY DIFFRACTION94
3.3396-4.20490.24081420.19553462X-RAY DIFFRACTION87
4.2049-26.78210.25111360.21533295X-RAY DIFFRACTION82

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