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- PDB-6faz: Crystal structure of the GluA2 ligand-binding domain (S1S2J) in c... -

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Basic information

Entry
Database: PDB / ID: 6faz
TitleCrystal structure of the GluA2 ligand-binding domain (S1S2J) in complex with the positive allosteric modulator TDPAM01 at 1.4 A resolution.
ComponentsGlutamate receptor 2
KeywordsMEMBRANE PROTEIN / AMPA receptor / GluA2 / Ligand-binding Domain / GluA2-S1S2J / positive allosteric modulator
Function / homology
Function and homology information


spine synapse / dendritic spine neck / dendritic spine head / cellular response to amine stimulus / perisynaptic space / Activation of AMPA receptors / ligand-gated monoatomic cation channel activity / AMPA glutamate receptor activity / response to lithium ion / Trafficking of GluR2-containing AMPA receptors ...spine synapse / dendritic spine neck / dendritic spine head / cellular response to amine stimulus / perisynaptic space / Activation of AMPA receptors / ligand-gated monoatomic cation channel activity / AMPA glutamate receptor activity / response to lithium ion / Trafficking of GluR2-containing AMPA receptors / kainate selective glutamate receptor activity / AMPA glutamate receptor complex / cellular response to glycine / extracellularly glutamate-gated ion channel activity / immunoglobulin binding / asymmetric synapse / ionotropic glutamate receptor complex / conditioned place preference / regulation of receptor recycling / glutamate receptor binding / Unblocking of NMDA receptors, glutamate binding and activation / positive regulation of synaptic transmission / regulation of synaptic transmission, glutamatergic / response to fungicide / cytoskeletal protein binding / glutamate-gated receptor activity / regulation of long-term synaptic depression / extracellular ligand-gated monoatomic ion channel activity / cellular response to brain-derived neurotrophic factor stimulus / presynaptic active zone membrane / glutamate-gated calcium ion channel activity / somatodendritic compartment / dendrite membrane / ionotropic glutamate receptor binding / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / ionotropic glutamate receptor signaling pathway / dendrite cytoplasm / synaptic membrane / dendritic shaft / SNARE binding / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / synaptic transmission, glutamatergic / PDZ domain binding / protein tetramerization / establishment of protein localization / postsynaptic density membrane / cerebral cortex development / modulation of chemical synaptic transmission / receptor internalization / Schaffer collateral - CA1 synapse / terminal bouton / synaptic vesicle / synaptic vesicle membrane / presynapse / signaling receptor activity / amyloid-beta binding / presynaptic membrane / growth cone / scaffold protein binding / perikaryon / chemical synaptic transmission / dendritic spine / postsynaptic membrane / neuron projection / postsynaptic density / axon / external side of plasma membrane / neuronal cell body / dendrite / synapse / protein kinase binding / protein-containing complex binding / glutamatergic synapse / 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 ...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 II / Periplasmic binding protein-like I / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Chem-D45 / GLUTAMIC ACID / DI(HYDROXYETHYL)ETHER / Glutamate receptor 2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsNielsen, L. / Laulumaa, S. / Kastrup, J.S.
CitationJournal: J. Med. Chem. / Year: 2018
Title: Enhancing Action of Positive Allosteric Modulators through the Design of Dimeric Compounds.
Authors: Drapier, T. / Geubelle, P. / Bouckaert, C. / Nielsen, L. / Laulumaa, S. / Goffin, E. / Dilly, S. / Francotte, P. / Hanson, J. / Pochet, L. / Kastrup, J.S. / Pirotte, B.
History
DepositionDec 18, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 21, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 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
Revision 1.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)60,90627
Polymers58,5572
Non-polymers2,34825
Water11,908661
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6090 Å2
ΔGint-94 kcal/mol
Surface area23850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.206, 121.458, 47.164
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

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Protein , 1 types, 2 molecules AB

#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.: 2
Source method: isolated from a genetically manipulated source
Details: Extracellular ligand-binding domain of GluA2, transmembrane regions were genetically removed and replaced with a Gly-Thr linker (residue 118-119). The sequence matches discontinuously with ...Details: Extracellular ligand-binding domain of GluA2, transmembrane regions were genetically removed and replaced with a Gly-Thr linker (residue 118-119). The sequence matches discontinuously with reference database (413-527, 653-797). Gly-Ala are cloning remanants.
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Gria2, Glur2 / Plasmid: pET22B(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): Origami B / References: UniProt: P19491

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Non-polymers , 9 types, 686 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#7: Chemical ChemComp-GLU / GLUTAMIC ACID


Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H9NO4
#8: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#9: Chemical ChemComp-D45 / 6,6'-(Ethane-1,2-diyl)bis(4-methyl-3,4-dihydro-2H-1,2,4-benzothiadiazine 1,1-dioxide)


Mass: 422.522 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H22N4O4S2
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 661 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.4 Å3/Da / Density % sol: 48.79 %
Crystal growTemperature: 280 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 15% PEG4000, 0.3 M ammonium sulfate, 0.1 M phosphate-citrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.9796 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 30, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 1.4→48.603 Å / Num. all: 110666 / Num. obs: 110666 / % possible obs: 100 % / Redundancy: 13.3 % / Biso Wilson estimate: 18.03 Å2 / Rpim(I) all: 0.015 / Rrim(I) all: 0.057 / Rsym value: 0.055 / Net I/av σ(I): 7.2 / Net I/σ(I): 19.6 / Num. measured all: 1470878
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
1.4-1.4813.40.6431.2213713159690.1810.6680.6433.8100
1.48-1.5713.50.3772205158151470.1050.3910.3775.8100
1.57-1.6713.40.2363.1191528142640.0660.2460.2368.2100
1.67-1.8112.70.1564.4168301133010.0450.1630.15611.2100
1.81-1.9812.50.1036.4152467122430.030.1070.10317100
1.98-2.2113.60.0748.6150729111230.0210.0770.07426.7100
2.21-2.5613.90.06110.313686898700.0170.0640.06133.1100
2.56-3.1313.60.04812.811450884120.0130.050.04841.8100
3.13-4.4313.60.03815.58967065740.0110.0390.03856.7100
4.43-48.60312.70.033164793637630.010.0340.03352.598.8

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Processing

Software
NameVersionClassification
PHENIXrefinement
SCALA3.3.22data scaling
PDB_EXTRACT3.24data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4N07

4n07


Resolution: 1.4→47.164 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 0.5 / Phase error: 16.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1675 5450 4.93 %
Rwork0.1364 105040 -
obs0.1379 110490 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 81.79 Å2 / Biso mean: 23.7221 Å2 / Biso min: 11.27 Å2
Refinement stepCycle: final / Resolution: 1.4→47.164 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4073 0 148 677 4898
Biso mean--33.55 33.58 -
Num. residues----523
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074549
X-RAY DIFFRACTIONf_angle_d0.9836154
X-RAY DIFFRACTIONf_chiral_restr0.077669
X-RAY DIFFRACTIONf_plane_restr0.006763
X-RAY DIFFRACTIONf_dihedral_angle_d20.5271785
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.4-1.41590.25751780.181434253603100
1.4159-1.43260.19971810.156634933674100
1.4326-1.450.22961620.1534443606100
1.45-1.46840.18211600.130434873647100
1.4684-1.48770.19041880.128434273615100
1.4877-1.50810.1881880.125634533641100
1.5081-1.52960.19491930.124134603653100
1.5296-1.55250.18682050.120834313636100
1.5525-1.57670.17651690.114635003669100
1.5767-1.60260.15611900.11134353625100
1.6026-1.63020.17261930.11134863679100
1.6302-1.65990.15791730.110834613634100
1.6599-1.69180.15711610.115335273688100
1.6918-1.72630.17661690.128134643633100
1.7263-1.76390.16351890.121834743663100
1.7639-1.80490.18561640.126235113675100
1.8049-1.850.16361900.120834633653100
1.85-1.90010.16042040.12134923696100
1.9001-1.9560.17091760.121434963672100
1.956-2.01910.17381770.125234903667100
2.0191-2.09130.16331830.129335033686100
2.0913-2.1750.14461890.125535003689100
2.175-2.2740.15231910.120635053696100
2.274-2.39390.16911820.126335293711100
2.3939-2.54390.16852070.135934893696100
2.5439-2.74030.15681770.140335563733100
2.7403-3.0160.16321810.145835793760100
3.016-3.45230.16791870.143635823769100
3.4523-4.3490.1461770.135136293806100
4.349-47.19080.1971660.17053749391598

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