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- PDB-6xsr: Crystal structure of GluA2 AMPA receptor in complex with trans-4-... -

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Basic information

Entry
Database: PDB / ID: 6xsr
TitleCrystal structure of GluA2 AMPA receptor in complex with trans-4-butylcyclohexane carboxylic acid (4-BCCA) inhibitor
ComponentsGlutamate receptor 2
KeywordsTRANSPORT PROTEIN / AMPA receptor / ion channels / synapse / BCCA
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
trans-4-butylcyclohexane-1-carboxylic acid / Glutamate receptor 2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.25 Å
AuthorsYelshanskaya, M.V. / Singh, A.K. / Sobolevsky, A.I.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)R01 NS083660 United States
CitationJournal: Br.J.Pharmacol. / Year: 2022
Title: Structural basis of AMPA receptor inhibition by trans-4-butylcyclohexane carboxylic acid.
Authors: Yelshanskaya, M.V. / Singh, A.K. / Narangoda, C. / Williams, R.S.B. / Kurnikova, M.G. / Sobolevsky, A.I.
History
DepositionJul 16, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 30, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 29, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)363,86310
Polymers362,6094
Non-polymers1,2536
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area26430 Å2
ΔGint-199 kcal/mol
Surface area138500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.790, 110.400, 600.140
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: 90652.359 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Gria2, Glur2 / 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-V8G / trans-4-butylcyclohexane-1-carboxylic acid


Mass: 184.275 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C11H20O2 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
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: 4.41 Å3/Da / Density % sol: 72.41 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 8-11% (w/v) PEG 8,000, 0.2 M magnesium acetate and 0.1 M sodium cacodylate (pH 6.3-6.7) or 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 / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 21, 2018
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 4.25→48.912 Å / Num. obs: 83453 / % possible obs: 99.6 % / Redundancy: 9.82 % / CC1/2: 0.99 / Rmerge(I) obs: 0.45 / Net I/σ(I): 9.35
Reflection shellResolution: 4.25→4.52 Å / Num. unique obs: 14923 / CC1/2: 0.61

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Processing

Software
NameVersionClassification
PHENIX(1.16_3549)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KG2

3kg2


Resolution: 4.25→48.912 Å / SU ML: 0.6 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 31.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2959 4184 5.01 %
Rwork0.2604 --
obs0.2622 83453 99.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 4.25→48.912 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23693 0 82 0 23775
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00224264
X-RAY DIFFRACTIONf_angle_d0.55832857
X-RAY DIFFRACTIONf_dihedral_angle_d5.68214331
X-RAY DIFFRACTIONf_chiral_restr0.0413728
X-RAY DIFFRACTIONf_plane_restr0.0044171
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.2502-4.29840.34081310.342541X-RAY DIFFRACTION100
4.2984-4.3490.35541430.352715X-RAY DIFFRACTION100
4.349-4.4020.38541410.35362672X-RAY DIFFRACTION100
4.402-4.45770.35881380.34982600X-RAY DIFFRACTION100
4.4577-4.51630.39571390.34932674X-RAY DIFFRACTION100
4.5163-4.57810.29811350.292623X-RAY DIFFRACTION99
4.5781-4.64340.34031440.342656X-RAY DIFFRACTION99
4.6434-4.71270.3821380.31432582X-RAY DIFFRACTION100
4.7127-4.78630.30761440.32710X-RAY DIFFRACTION100
4.7863-4.86470.37051350.31472638X-RAY DIFFRACTION100
4.8647-4.94850.31591410.30942599X-RAY DIFFRACTION100
4.9485-5.03840.35011400.30742688X-RAY DIFFRACTION100
5.0384-5.13520.33251460.30852695X-RAY DIFFRACTION100
5.1352-5.23990.34141320.3152608X-RAY DIFFRACTION100
5.2399-5.35370.271420.272643X-RAY DIFFRACTION100
5.3537-5.47810.27821440.27822667X-RAY DIFFRACTION100
5.4781-5.61490.27581390.27582611X-RAY DIFFRACTION100
5.6149-5.76650.31221410.30412731X-RAY DIFFRACTION99
5.7665-5.93590.30191360.30192571X-RAY DIFFRACTION100
5.9359-6.12710.36681500.29862718X-RAY DIFFRACTION100
6.1271-6.34570.33911330.28852601X-RAY DIFFRACTION100
6.3457-6.59910.30291440.28782667X-RAY DIFFRACTION100
6.5991-6.89870.26891400.26892650X-RAY DIFFRACTION100
6.8987-7.26130.28981410.26962659X-RAY DIFFRACTION100
7.2613-7.71460.29111390.26382614X-RAY DIFFRACTION98
7.5-100.34271360.2622623X-RAY DIFFRACTION99
7.7146-8.30760.30031350.24242625X-RAY DIFFRACTION100
7.9-100.23731370.1912632X-RAY DIFFRACTION99
8-9.13870.23551430.21022665X-RAY DIFFRACTION100

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