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- PDB-5ng9: Crystal structure of the GluA2 ligand-binding domain (S1S2J) in c... -

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Basic information

Entry
Database: PDB / ID: 5ng9
TitleCrystal structure of the GluA2 ligand-binding domain (S1S2J) in complex with agonist CIP-AS at 1.15 A resolution.
ComponentsGlutamate receptor 2
KeywordsMEMBRANE PROTEIN / IONOTROPIC GLUTAMATE RECEPTOR / AMPA RECEPTOR / LIGAND-BINDING DOMAIN / GLUA2 / GLUR2 / AGONIST
Function / homology
Function and homology information


spine synapse / dendritic spine neck / dendritic spine head / Activation of AMPA receptors / perisynaptic space / AMPA glutamate receptor activity / Trafficking of GluR2-containing AMPA receptors / response to lithium ion / immunoglobulin binding / AMPA glutamate receptor complex ...spine synapse / dendritic spine neck / dendritic spine head / Activation of AMPA receptors / perisynaptic space / AMPA glutamate receptor activity / Trafficking of GluR2-containing AMPA receptors / response to lithium ion / immunoglobulin binding / AMPA glutamate receptor complex / kainate selective glutamate receptor activity / ionotropic glutamate receptor complex / extracellularly glutamate-gated ion channel activity / 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 / glutamate-gated receptor activity / presynaptic active zone membrane / response to fungicide / regulation of synaptic transmission, glutamatergic / somatodendritic compartment / cellular response to brain-derived neurotrophic factor stimulus / dendrite membrane / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / cytoskeletal protein binding / ionotropic glutamate receptor signaling pathway / dendrite cytoplasm / SNARE binding / dendritic shaft / synaptic membrane / synaptic transmission, glutamatergic / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / PDZ domain binding / protein tetramerization / postsynaptic density membrane / ionotropic glutamate receptor binding / Schaffer collateral - CA1 synapse / modulation of chemical synaptic transmission / establishment of protein localization / terminal bouton / receptor internalization / cerebral cortex development / synaptic vesicle membrane / synaptic vesicle / presynapse / presynaptic membrane / signaling receptor activity / amyloid-beta binding / growth cone / scaffold protein binding / chemical synaptic transmission / postsynaptic membrane / perikaryon / dendritic spine / postsynaptic density / neuron projection / axon / neuronal cell body / glutamatergic synapse / synapse / dendrite / protein-containing complex binding / endoplasmic reticulum membrane / protein kinase binding / cell surface / endoplasmic reticulum / protein-containing complex / identical protein binding / 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-8VN / Chem-8WQ / CITRATE ANION / : / Glutamate receptor 2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.15 Å
AuthorsLaulumaa, S. / Frydenvang, K.A. / Winther, S. / Kastrup, J.S.
CitationJournal: ACS Chem Neurosci / Year: 2017
Title: Structure and Affinity of Two Bicyclic Glutamate Analogues at AMPA and Kainate Receptors.
Authors: Mllerud, S. / Pinto, A. / Marconi, L. / Frydenvang, K. / Thorsen, T.S. / Laulumaa, S. / Venskutonyte, R. / Winther, S. / Moral, A.M.C. / Tamborini, L. / Conti, P. / Pickering, D.S. / Kastrup, J.S.
History
DepositionMar 17, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 26, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glutamate receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,44710
Polymers29,2791
Non-polymers1,1699
Water7,873437
1
A: Glutamate receptor 2
hetero molecules

A: Glutamate receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,89520
Polymers58,5572
Non-polymers2,33718
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_775-x+2,-y+2,z1
Buried area4540 Å2
ΔGint-66 kcal/mol
Surface area25090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.218, 88.140, 47.958
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-593-

HOH

21A-734-

HOH

31A-827-

HOH

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Components

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Protein , 1 types, 1 molecules A

#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: 29278.732 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: THE PROTEIN CRYSTALLIZED IS THE EXTRACELLULAR LIGAND-BINDING DOMIAN OF GLUA2. TRANSMEMBRANE REGIONS WERE REPLACED WITH A GLY-THR LINKER (118-119). SEQUENCE MATCHES DISCONTINUOUSLY WITH THE ...Details: THE PROTEIN CRYSTALLIZED IS THE EXTRACELLULAR LIGAND-BINDING DOMIAN OF GLUA2. TRANSMEMBRANE REGIONS WERE REPLACED WITH A GLY-THR LINKER (118-119). SEQUENCE MATCHES DISCONTINUOUSLY WITH THE REFERENCE DATABASE (413-527, 653-797). RESIDUES 1-2 ARE CLONING REMNANTS.
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Gria2, Glur2 / Production host: Escherichia coli (E. coli) / Variant (production host): Origami B (DE3) / References: UniProt: P19491

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Non-polymers , 7 types, 446 molecules

#2: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H5O7
#3: Chemical ChemComp-LI / LITHIUM ION


Mass: 6.941 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Li
#4: Chemical ChemComp-8VN / (3~{a}~{S},4~{S},6~{a}~{R})-4,5,6,6~{a}-tetrahydro-3~{a}~{H}-pyrrolo[3,4-d][1,2]oxazole-3,4-dicarboxylic acid


Mass: 200.149 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H8N2O5
#5: Chemical ChemComp-8WQ / (2~{S},3~{R},4~{R})-3-(carboxycarbonyl)-4-oxidanyl-pyrrolidine-2-carboxylic acid


Mass: 203.149 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H9NO6
#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 437 / 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: 2.25 Å3/Da / Density % sol: 45.33 %
Crystal growTemperature: 279 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 15.2% PEG4000, 0.1 M lithium sulfate, 0.1 M phosphate-citrate buffer

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 21, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.15→47.96 Å / Num. obs: 93257 / % possible obs: 98.9 % / Redundancy: 5.8 % / Biso Wilson estimate: 8.08 Å2 / Rpim(I) all: 0.019 / Rrim(I) all: 0.045 / Rsym value: 0.041 / Net I/σ(I): 22.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsRpim(I) allRrim(I) allRsym value% possible all
1.15-1.214.50.2293.40.1190.2590.22992.5
1.21-1.295.80.1814.30.0810.1990.181100
1.29-1.3760.1315.90.0580.1440.131100
1.37-1.4860.09680.0420.1050.096100
1.48-1.636.10.06611.40.0290.0720.066100
1.63-1.826.10.05114.20.0220.0560.051100
1.82-2.16.10.038170.0170.0420.038100
2.1-2.576.10.03219.50.0140.0350.032100
2.57-3.646.10.02622.10.0120.0290.026100
3.64-47.9585.60.02227.50.010.0240.02298.3

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Processing

Software
NameVersionClassification
PHENIXrefinement
SCALA3.3.20data scaling
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1M5B

1m5b


Resolution: 1.15→37.98 Å / SU ML: 0.06 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 9.37
RfactorNum. reflection% reflection
Rfree0.133 4676 5.02 %
Rwork0.109 --
obs0.11 93190 98.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 13.18 Å2
Refinement stepCycle: LAST / Resolution: 1.15→37.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2045 0 76 437 2558
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092354
X-RAY DIFFRACTIONf_angle_d1.1773211
X-RAY DIFFRACTIONf_dihedral_angle_d13.328940
X-RAY DIFFRACTIONf_chiral_restr0.089351
X-RAY DIFFRACTIONf_plane_restr0.008407
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.15-1.16310.15981300.14752497X-RAY DIFFRACTION85
1.1631-1.17680.15851380.13192712X-RAY DIFFRACTION92
1.1768-1.19110.13311380.11022822X-RAY DIFFRACTION94
1.1911-1.20620.14451490.10862830X-RAY DIFFRACTION96
1.2062-1.22210.13741670.1092911X-RAY DIFFRACTION100
1.2221-1.23880.14181420.10612959X-RAY DIFFRACTION100
1.2388-1.25650.1351740.10232952X-RAY DIFFRACTION100
1.2565-1.27530.13221770.10012901X-RAY DIFFRACTION100
1.2753-1.29520.12741790.09392970X-RAY DIFFRACTION100
1.2952-1.31640.12451400.09062949X-RAY DIFFRACTION100
1.3164-1.33910.12741740.0922960X-RAY DIFFRACTION100
1.3391-1.36350.13111890.08792923X-RAY DIFFRACTION100
1.3635-1.38970.11151370.08742966X-RAY DIFFRACTION100
1.3897-1.41810.10741570.08472981X-RAY DIFFRACTION100
1.4181-1.44890.12241420.08282986X-RAY DIFFRACTION100
1.4489-1.48260.12991510.08422967X-RAY DIFFRACTION100
1.4826-1.51970.12611560.08142987X-RAY DIFFRACTION100
1.5197-1.56080.11521440.08242945X-RAY DIFFRACTION100
1.5608-1.60670.10551600.08053003X-RAY DIFFRACTION100
1.6067-1.65860.10751580.0832952X-RAY DIFFRACTION100
1.6586-1.71780.1221490.08743005X-RAY DIFFRACTION100
1.7178-1.78660.13681520.09423001X-RAY DIFFRACTION100
1.7866-1.86790.11651580.0962972X-RAY DIFFRACTION100
1.8679-1.96640.1311720.10033000X-RAY DIFFRACTION100
1.9664-2.08960.121720.10212999X-RAY DIFFRACTION100
2.0896-2.25090.12681460.10433027X-RAY DIFFRACTION100
2.2509-2.47740.14551350.1163036X-RAY DIFFRACTION100
2.4774-2.83580.13241680.1273063X-RAY DIFFRACTION100
2.8358-3.57240.14881520.13093079X-RAY DIFFRACTION100
3.5724-38.00440.15491700.14293159X-RAY DIFFRACTION98

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