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- PDB-5l1e: AMPA subtype ionotropic glutamate receptor GluA2 in complex with ... -

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Basic information

Entry
Database: PDB / ID: 5l1e
TitleAMPA subtype ionotropic glutamate receptor GluA2 in complex with noncompetitive inhibitor CP465022
ComponentsGlutamate receptor 2
KeywordsTRANSPORT PROTEIN/INHIBITOR / Transporter / MEMBRANE PROTEIN / TRANSPORT PROTEIN / TRANSPORT PROTEIN-INHIBITOR complex
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 / extracellularly glutamate-gated ion channel activity ...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 / extracellularly glutamate-gated ion channel activity / immunoglobulin binding / AMPA glutamate receptor complex / kainate selective glutamate receptor activity / ionotropic glutamate receptor complex / cellular response to glycine / asymmetric synapse / regulation of receptor recycling / Unblocking of NMDA receptors, glutamate binding and activation / glutamate receptor binding / positive regulation of synaptic transmission / extracellular ligand-gated monoatomic ion channel activity / glutamate-gated receptor activity / response to fungicide / glutamate-gated calcium ion channel activity / presynaptic active zone membrane / regulation of synaptic transmission, glutamatergic / ionotropic glutamate receptor binding / somatodendritic compartment / dendrite membrane / cellular response to brain-derived neurotrophic factor stimulus / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / cytoskeletal protein binding / dendrite cytoplasm / ionotropic glutamate receptor signaling pathway / SNARE binding / dendritic shaft / synaptic transmission, glutamatergic / synaptic membrane / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / PDZ domain binding / protein tetramerization / postsynaptic density membrane / establishment of protein localization / modulation of chemical synaptic transmission / Schaffer collateral - CA1 synapse / terminal bouton / receptor internalization / cerebral cortex development / synaptic vesicle membrane / synaptic vesicle / presynapse / signaling receptor activity / presynaptic membrane / amyloid-beta binding / growth cone / scaffold protein binding / chemical synaptic transmission / perikaryon / postsynaptic membrane / dendritic spine / postsynaptic density / neuron projection / axon / neuronal cell body / glutamatergic synapse / dendrite / synapse / protein-containing complex binding / protein kinase binding / 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 / Periplasmic binding protein-like I
Similarity search - Domain/homology
Chem-6ZQ / Glutamate receptor 2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.37 Å
AuthorsYelshanskaya, M.V. / Singh, A.K. / Sampson, J.M. / Sobolevsky, A.I.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)NS083660, United States
CitationJournal: Neuron / Year: 2016
Title: Structural Bases of Noncompetitive Inhibition of AMPA-Subtype Ionotropic Glutamate Receptors by Antiepileptic Drugs.
Authors: Yelshanskaya, M.V. / Singh, A.K. / Sampson, J.M. / Narangoda, C. / Kurnikova, M. / Sobolevsky, A.I.
History
DepositionJul 29, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 19, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)361,96812
Polymers359,2234
Non-polymers2,7458
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area26770 Å2
ΔGint-213 kcal/mol
Surface area138090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.677, 109.858, 602.462
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 / 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: 89805.734 Da / Num. of mol.: 4
Fragment: UNP residues 25-847, with deletions of 397-398, 402-405, 566-587
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Gria2, Glur2 / Plasmid: pEG BacMam / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: P19491
#2: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical
ChemComp-6ZQ / 3-(2-chlorophenyl)-2-(2-{6-[(diethylamino)methyl]pyridin-2-yl}ethyl)-6-fluoroquinazolin-4(3H)-one


Mass: 464.962 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C26H26ClFN4O

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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: 4.31 Å3/Da / Density % sol: 71.44 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 11-14% (w/v) PEG 6,000, 0.1 M ammonium phosphate and 0.1 M TRIS (pH 7.9-8.0)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 6, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 4.37→50 Å / Num. obs: 75334 / % possible obs: 98 % / Redundancy: 4.94 % / Rmerge(I) obs: 0.102 / Net I/σ(I): 8.15
Reflection shellHighest resolution: 4.37 Å / Rmerge(I) obs: 1.502

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KG2

3kg2


Resolution: 4.37→49.016 Å / SU ML: 0.83 / Cross valid method: FREE R-VALUE / σ(F): 1.12 / Phase error: 31.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.292 3785 5.02 %
Rwork0.239 --
obs0.2415 75333 97.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 4.37→49.016 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23903 0 189 0 24092
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00224603
X-RAY DIFFRACTIONf_angle_d0.53933320
X-RAY DIFFRACTIONf_dihedral_angle_d10.64214487
X-RAY DIFFRACTIONf_chiral_restr0.0393739
X-RAY DIFFRACTIONf_plane_restr0.0044209
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.3699-4.42520.42591000.39531999X-RAY DIFFRACTION73
4.4252-4.48340.43281400.37222684X-RAY DIFFRACTION100
4.4834-4.54480.37291410.3592659X-RAY DIFFRACTION100
4.5448-4.60970.40951460.35052750X-RAY DIFFRACTION99
4.6097-4.67840.35141420.33152691X-RAY DIFFRACTION100
4.6784-4.75150.35731460.33272656X-RAY DIFFRACTION100
4.7515-4.82930.35721430.30562698X-RAY DIFFRACTION99
4.8293-4.91250.32421440.29222726X-RAY DIFFRACTION99
4.9125-5.00170.32651410.27872689X-RAY DIFFRACTION100
5.0017-5.09780.33661410.27252674X-RAY DIFFRACTION99
5.0978-5.20180.32451340.27312605X-RAY DIFFRACTION96
5.2018-5.31480.30941360.26372569X-RAY DIFFRACTION96
5.3148-5.43820.29821490.25582742X-RAY DIFFRACTION100
5.4382-5.57410.31791390.2392646X-RAY DIFFRACTION100
5.5741-5.72450.28831470.23612729X-RAY DIFFRACTION100
5.7245-5.89270.29061390.24082653X-RAY DIFFRACTION100
5.8927-6.08260.32911450.25612736X-RAY DIFFRACTION100
6.0826-6.29960.32621420.23052698X-RAY DIFFRACTION100
6.2996-6.55120.32821480.21762713X-RAY DIFFRACTION100
6.5512-6.84860.28871330.21522647X-RAY DIFFRACTION98
6.8486-7.20860.31151420.21842618X-RAY DIFFRACTION96
7.2086-7.65870.27441460.18952681X-RAY DIFFRACTION100
7.6587-8.24750.27721380.1862671X-RAY DIFFRACTION99
8.2475-9.07270.26011430.17292680X-RAY DIFFRACTION99
9.0727-10.37470.23821400.1572608X-RAY DIFFRACTION96
10.3747-13.03030.21541400.1732685X-RAY DIFFRACTION99
13.0303-49.01870.31531400.32682641X-RAY DIFFRACTION98

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