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- PDB-3o6g: Ligand-binding domain of GluA2 (flip) ionotropic glutamate recept... -

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Basic information

Entry
Database: PDB / ID: 3o6g
TitleLigand-binding domain of GluA2 (flip) ionotropic glutamate receptor in complex with an allosteric modulator
ComponentsGlutamate receptor 2GRIA2
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 / 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
GLUTAMIC ACID / Chem-O27 / Glutamate receptor 2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsMaclean, J.K.F. / Campbell, R.A. / Cumming, I.A. / Gillen, K.J. / Gillespie, J. / Jamieson, C. / Kazemier, B. / Kiczun, M. / Lamont, Y. / Lyons, A.J. ...Maclean, J.K.F. / Campbell, R.A. / Cumming, I.A. / Gillen, K.J. / Gillespie, J. / Jamieson, C. / Kazemier, B. / Kiczun, M. / Lamont, Y. / Lyons, A.J. / Martin, F. / Moir, E.M. / Morrow, J.A. / Pantling, J. / Rankovic, Z. / Smith, L.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2010
Title: A novel series of positive modulators of the AMPA receptor: structure-based lead optimization.
Authors: Jamieson, C. / Campbell, R.A. / Cumming, I.A. / Gillen, K.J. / Gillespie, J. / Kazemier, B. / Kiczun, M. / Lamont, Y. / Lyons, A.J. / Maclean, J.K. / Martin, F. / Moir, E.M. / Morrow, J.A. / ...Authors: Jamieson, C. / Campbell, R.A. / Cumming, I.A. / Gillen, K.J. / Gillespie, J. / Kazemier, B. / Kiczun, M. / Lamont, Y. / Lyons, A.J. / Maclean, J.K. / Martin, F. / Moir, E.M. / Morrow, J.A. / Pantling, J. / Rankovic, Z. / Smith, L.
History
DepositionJul 29, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glutamate receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,35710
Polymers29,1781
Non-polymers1,1799
Water7,044391
1
A: Glutamate receptor 2
hetero molecules

A: Glutamate receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,71420
Polymers58,3552
Non-polymers2,35818
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Unit cell
Length a, b, c (Å)64.090, 87.180, 47.320
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 / GRIA2 / 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-32a / Production host: Escherichia coli (E. coli) / Strain (production host): Origami B(DE3) / References: UniProt: P19491

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Non-polymers , 5 types, 400 molecules

#2: Chemical ChemComp-GLU / GLUTAMIC ACID / 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 / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-O27 / N-[(3R)-pyrrolidin-3-yl]-2-({[3-(trifluoromethyl)-4,5,6,7-tetrahydro-1H-indazol-1-yl]acetyl}amino)-4,5,6,7-tetrahydro-1-benzothiophene-3-carboxamide


Type: peptide-like / Mass: 495.561 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H28F3N5O2S
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 391 / 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: 2.27 Å3/Da / Density % sol: 45.7 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 17% PEG 4000, 100mM Sodium Cacodylate pH 4.0, 50mM Lithium Sulphate, 2.5% Glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54178 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Feb 27, 2006
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.8→87.039 Å / Num. all: 28946 / Num. obs: 24720 / % possible obs: 98 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Biso Wilson estimate: 24.1 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 13.9
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.303 / Mean I/σ(I) obs: 2.1 / % possible all: 88

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Processing

Software
NameVersionClassification
CrystalCleardata collection
AMoREphasing
REFMAC5.2.0019refinement
CrystalCleardata reduction
CrystalCleardata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→87.039 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.932 / SU B: 2.783 / SU ML: 0.088 / Cross valid method: THROUGHOUT / ESU R Free: 0.138 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22273 1231 5 %RANDOM
Rwork0.18916 ---
all0.19078 23489 --
obs0.19078 23489 97.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.56 Å2
Baniso -1Baniso -2Baniso -3
1--1.19 Å20 Å20 Å2
2--1.61 Å20 Å2
3----0.42 Å2
Refinement stepCycle: LAST / Resolution: 1.8→87.039 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2043 0 75 391 2509
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0222318
X-RAY DIFFRACTIONr_bond_other_d0.0010.021628
X-RAY DIFFRACTIONr_angle_refined_deg1.1712.0083150
X-RAY DIFFRACTIONr_angle_other_deg0.8493.0014007
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3065306
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.16424.58396
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.47115446
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2991512
X-RAY DIFFRACTIONr_chiral_restr0.0690.2336
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022549
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02445
X-RAY DIFFRACTIONr_nbd_refined0.20.2451
X-RAY DIFFRACTIONr_nbd_other0.1850.21695
X-RAY DIFFRACTIONr_nbtor_refined0.1730.21099
X-RAY DIFFRACTIONr_nbtor_other0.0860.21130
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1430.2255
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2260.237
X-RAY DIFFRACTIONr_symmetry_vdw_other0.170.279
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1770.231
X-RAY DIFFRACTIONr_mcbond_it1.06721824
X-RAY DIFFRACTIONr_mcbond_other0.1752567
X-RAY DIFFRACTIONr_mcangle_it1.23432238
X-RAY DIFFRACTIONr_scbond_it1.83841134
X-RAY DIFFRACTIONr_scangle_it2.5346890
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.304 87 -
Rwork0.29 1444 -
obs--83.25 %

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