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- PDB-3o29: Ligand-binding domain of GluA2 (flip) ionotropic glutamate recept... -

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Basic information

Entry
Database: PDB / ID: 3o29
TitleLigand-binding domain of GluA2 (flip) ionotropic glutamate receptor in complex with an allosteric modulator
ComponentsGlutamate receptor 2
KeywordsTRANSPORT PROTEIN / Membrane Protein / Fusion protein / chimera protein
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 / terminal bouton / Schaffer collateral - CA1 synapse / 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 ...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
GLUTAMIC ACID / Chem-O29 / Glutamate receptor 2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.02 Å
AuthorsMaclean, J.K.F. / Basten, S. / Campbell, R.A. / Cumming, I.A. / Gillen, K.J. / Gillespie, J. / Jamieson, C. / Kazemier, B. / Kiczun, M. / Lamont, Y. ...Maclean, J.K.F. / Basten, S. / Campbell, R.A. / Cumming, I.A. / Gillen, K.J. / Gillespie, J. / Jamieson, C. / Kazemier, B. / Kiczun, M. / Lamont, Y. / Lyons, A.J. / Moir, E.M. / Morrow, J.A. / Papakosta, M. / Rankovic, Z. / Smith, L.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2010
Title: A novel series of positive modulators of the AMPA receptor: discovery and structure based hit-to-lead studies.
Authors: Jamieson, C. / Basten, S. / Campbell, R.A. / Cumming, I.A. / Gillen, K.J. / Gillespie, J. / Kazemier, B. / Kiczun, M. / Lamont, Y. / Lyons, A.J. / Maclean, J.K. / Moir, E.M. / Morrow, J.A. / ...Authors: Jamieson, C. / Basten, S. / Campbell, R.A. / Cumming, I.A. / Gillen, K.J. / Gillespie, J. / Kazemier, B. / Kiczun, M. / Lamont, Y. / Lyons, A.J. / Maclean, J.K. / Moir, E.M. / Morrow, J.A. / Papakosta, M. / Rankovic, Z. / Smith, L.
History
DepositionJul 22, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 15, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 9, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.3Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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

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Assembly

Deposited unit
A: Glutamate receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,3839
Polymers29,1781
Non-polymers1,2058
Water4,522251
1
A: Glutamate receptor 2
hetero molecules

A: Glutamate receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,76618
Polymers58,3552
Non-polymers2,41016
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area4190 Å2
ΔGint-55 kcal/mol
Surface area23580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.127, 88.518, 47.336
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Glutamate receptor 2 / GluR-2 / GluR-B / GluR-K2 / Glutamate receptor ionotropic / AMPA 2 / GluA2 / AMPA-selective ...GluR-2 / GluR-B / GluR-K2 / Glutamate receptor ionotropic / AMPA 2 / GluA2 / AMPA-selective glutamate receptor 2


Mass: 29177.670 Da / Num. of mol.: 1
Fragment: Ligand binding domain, UNP residues 413 to 527 and 653 to 796
Source method: isolated from a genetically manipulated source
Details: S1-S2 fusion in which Gly118 and Thr119 replace a membrane-spanning region
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Gria2, Glur2 / Plasmid: pET-23a / Production host: Escherichia coli (E. coli) / Strain (production host): Origami B(DE3) / References: UniProt: P19491

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Non-polymers , 5 types, 259 molecules

#2: Chemical ChemComp-GLU / GLUTAMIC ACID


Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H9NO4
#3: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-O29 / N-[2-(dimethylamino)ethyl]-2-({[3-(trifluoromethyl)-4,5,6,7-tetrahydro-1H-indazol-1-yl]acetyl}amino)-4,5,6,7-tetrahydro-1-benzothiophene-3-carboxamide


Mass: 497.577 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H30F3N5O2S
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 251 / 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: 2.3 Å3/Da / Density % sol: 46.57 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 12% PEG 4000, 100mM Sodium Cacodylate pH 4.5, 50mM Lithium Sulphate, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.931 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jul 4, 2005
RadiationMonochromator: Diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.931 Å / Relative weight: 1
ReflectionResolution: 2→25 Å / Num. all: 17620 / Num. obs: 17620 / % possible obs: 96.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.4 % / Biso Wilson estimate: 27.5 Å2 / Rmerge(I) obs: 0.071 / Net I/σ(I): 16.4
Reflection shellResolution: 2→2.07 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.409 / Mean I/σ(I) obs: 2.5 / Num. unique all: 1467 / % possible all: 81.7

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Processing

Software
NameVersionClassification
HKL-2000data collection
AMoREphasing
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.02→25 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.926 / SU B: 4.885 / SU ML: 0.134 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.201 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24977 878 5.1 %RANDOM
Rwork0.16993 ---
all0.17391 16399 --
obs0.17391 16399 94.08 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.308 Å2
Baniso -1Baniso -2Baniso -3
1--1.77 Å20 Å20 Å2
2--2.09 Å20 Å2
3----0.33 Å2
Refinement stepCycle: LAST / Resolution: 2.02→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2042 0 78 251 2371
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_refined_d0.018
X-RAY DIFFRACTIONr_angle_refined_deg1.845
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.584
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.722
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.527
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.569
X-RAY DIFFRACTIONr_chiral_restr0.111
X-RAY DIFFRACTIONr_gen_planes_refined0.007
X-RAY DIFFRACTIONr_nbd_refined0.221
X-RAY DIFFRACTIONr_nbtor_refined0.306
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.178
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.253
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.239
X-RAY DIFFRACTIONr_mcbond_it1.052
X-RAY DIFFRACTIONr_mcangle_it1.595
X-RAY DIFFRACTIONr_scbond_it2.46
X-RAY DIFFRACTIONr_scangle_it3.876
LS refinement shellResolution: 2.018→2.07 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.383 49 -
Rwork0.235 815 -
obs--64.38 %

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