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- PDB-4isu: Crystal structure of the GluA2 ligand-binding domain (S1S2J) in c... -

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Basic information

Entry
Database: PDB / ID: 4isu
TitleCrystal structure of the GluA2 ligand-binding domain (S1S2J) in complex with the antagonist (2R)-IKM-159 at 2.3A resolution.
ComponentsGlutamate receptor 2GRIA2
Keywordsmembrane protein/antagonist / AMPA receptor ligand-binding domain / GluR2-S1S2J / antagonist / membrane protein / membrane protein-antagonist complex
Function / homology
Function and homology information


spine synapse / dendritic spine neck / dendritic spine head / Activation of AMPA receptors / response to lithium ion / perisynaptic space / cellular response to glycine / AMPA glutamate receptor activity / Trafficking of GluR2-containing AMPA receptors / immunoglobulin binding ...spine synapse / dendritic spine neck / dendritic spine head / Activation of AMPA receptors / response to lithium ion / perisynaptic space / cellular response to glycine / AMPA glutamate receptor activity / Trafficking of GluR2-containing AMPA receptors / immunoglobulin binding / AMPA glutamate receptor complex / kainate selective glutamate receptor activity / ionotropic glutamate receptor complex / extracellularly glutamate-gated ion channel activity / 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 / cellular response to brain-derived neurotrophic factor stimulus / somatodendritic compartment / dendrite membrane / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / ionotropic glutamate receptor binding / ionotropic glutamate receptor signaling pathway / dendrite cytoplasm / cytoskeletal protein binding / SNARE binding / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / dendritic shaft / synaptic membrane / synaptic transmission, glutamatergic / PDZ domain binding / postsynaptic density membrane / protein tetramerization / modulation of chemical synaptic transmission / Schaffer collateral - CA1 synapse / establishment of protein localization / terminal bouton / receptor internalization / synaptic vesicle membrane / cerebral cortex development / synaptic vesicle / presynapse / signaling receptor activity / presynaptic membrane / amyloid-beta binding / growth cone / perikaryon / chemical synaptic transmission / scaffold protein binding / postsynaptic membrane / dendritic spine / postsynaptic density / neuron projection / axon / neuronal cell body / dendrite / synapse / glutamatergic synapse / protein-containing complex binding / endoplasmic reticulum membrane / protein kinase binding / cell surface / endoplasmic reticulum / protein-containing complex / membrane / identical protein binding / 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-IKM / Glutamate receptor 2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsJuknaite, L. / Frydenvang, K. / Kastrup, J.S.
CitationJournal: J.Med.Chem. / Year: 2013
Title: Studies on an (S)-2-amino-3-(3-hydroxy-5-methyl-4-isoxazolyl)propionic acid (AMPA) receptor antagonist IKM-159: asymmetric synthesis, neuroactivity, and structural characterization.
Authors: Juknaite, L. / Sugamata, Y. / Tokiwa, K. / Ishikawa, Y. / Takamizawa, S. / Eng, A. / Sakai, R. / Pickering, D.S. / Frydenvang, K. / Swanson, G.T. / Kastrup, J.S. / Oikawa, M.
History
DepositionJan 17, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 20, 2013Provider: repository / Type: Initial release
Revision 1.1May 22, 2013Group: Database references
Revision 1.2Aug 16, 2017Group: Data collection / Refinement description / Source and taxonomy
Category: diffrn_source / entity_src_gen / software / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Sep 20, 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)118,31120
Polymers116,8874
Non-polymers1,42516
Water8,035446
1
A: Glutamate receptor 2
C: Glutamate receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,15610
Polymers58,4432
Non-polymers7128
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Glutamate receptor 2
B: Glutamate receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,15610
Polymers58,4432
Non-polymers7128
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Glutamate receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,6715
Polymers29,2221
Non-polymers4494
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Glutamate receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3894
Polymers29,2221
Non-polymers1673
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
C: Glutamate receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,4855
Polymers29,2221
Non-polymers2634
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
B: Glutamate receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7676
Polymers29,2221
Non-polymers5455
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)62.514, 88.773, 194.456
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Glutamate receptor 2 / GRIA2 / 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: 29221.682 Da / Num. of mol.: 4 / Fragment: Ligand-binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Glur2, Gria2 / Plasmid: pET-22b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): Origami B (DE3) / References: UniProt: P19491
#2: Chemical ChemComp-IKM / (4aS,5aR,6R,8aS,8bS)-5a-(carboxymethyl)-8-oxo-2,4a,5a,6,7,8,8a,8b-octahydro-1H-pyrrolo[3',4':4,5]furo[3,2-b]pyridine-6-carboxylic acid / IKM-159


Mass: 282.249 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H14N2O6
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 446 / 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: 2.31 Å3/Da / Density % sol: 46.71 %
Crystal growTemperature: 280 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 20% PEG4000, 0.1M Lithium sulfate, 0.1M phosphate-citrate pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 280K

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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: Feb 24, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→97.235 Å / Num. obs: 48097 / % possible obs: 98.3 % / Redundancy: 3.9 % / Biso Wilson estimate: 21 Å2 / Rsym value: 0.056 / Net I/σ(I): 14.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.3-2.422.90.1275.41925265420.12793.2
2.42-2.574.10.1096.12704766660.10999.9
2.57-2.754.10.0887.62575562960.08899.8
2.75-2.974.10.07582414258610.07599.6
2.97-3.254.10.0649.32206153570.06499.6
3.25-3.644.10.053122026949080.05399.3
3.64-4.24.10.04713.41781143210.04798.9
4.2-5.144.10.04213.51508936680.04298.6
5.14-7.274.10.03815.11166028710.03897.9
7.27-28.7753.90.02717620516070.02794.9

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Processing

Software
NameVersionClassificationNB
SCALA3.3.15data scaling
PHENIX1.7.1_743refinement
PDB_EXTRACT3.11data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1N0T molA

1n0t


Resolution: 2.3→29.15 Å / Occupancy max: 1 / Occupancy min: 0.23 / FOM work R set: 0.8194 / SU ML: 0.71 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 24.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2579 2410 5.02 %RANDOM
Rwork0.1854 ---
obs0.1891 48021 98.05 %-
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 22.927 Å2 / ksol: 0.376 e/Å3
Displacement parametersBiso max: 91.79 Å2 / Biso mean: 22.9895 Å2 / Biso min: 7.15 Å2
Baniso -1Baniso -2Baniso -3
1--1.944 Å2-0 Å20 Å2
2---4.3507 Å20 Å2
3---6.2947 Å2
Refinement stepCycle: LAST / Resolution: 2.3→29.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8093 0 78 446 8617
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0078353
X-RAY DIFFRACTIONf_angle_d1.04411248
X-RAY DIFFRACTIONf_chiral_restr0.0681241
X-RAY DIFFRACTIONf_plane_restr0.0041404
X-RAY DIFFRACTIONf_dihedral_angle_d14.9333132
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 17

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection allNum. reflection obs% reflection obs (%)
2.3-2.34690.28221210.170422732394227384
2.3469-2.39790.33011480.193926512799265198
2.3979-2.45370.32481450.2145266928142669100
2.4537-2.5150.31481400.2116270228422702100
2.515-2.5830.30711560.2038268328392683100
2.583-2.65890.3071480.2076267328212674100
2.6589-2.74470.29521460.2034268828342688100
2.7447-2.84270.30141610.2025271328742714100
2.8427-2.95640.28111380.205726932831269399
2.9564-3.09090.30621530.202926832836268399
3.0909-3.25360.26441400.196827052845270599
3.2536-3.45720.23821490.186726962845269699
3.4572-3.72360.25421370.18127222859272299
3.7236-4.09740.21491320.158927362868273699
4.0974-4.68820.16721360.137827242860272498
4.6882-5.89860.23811160.174727872903278998
5.8986-29.1520.2161440.192628132957282996

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