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- PDB-3rn8: Crystal Structure of iGluR2 Ligand Binding Domain and Symmetrical... -

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Basic information

Entry
Database: PDB / ID: 3rn8
TitleCrystal Structure of iGluR2 Ligand Binding Domain and Symmetrical Carboxyl Containing Potentiator
ComponentsGlutamate receptor 2
KeywordsTRANSPORT PROTEIN / glutamate receptor potentiator complex / ligand gated ion channel / membrane
Function / homology
Function and homology information


Activation of AMPA receptors / postsynaptic endocytic zone / Trafficking of GluR2-containing AMPA receptors / AMPA glutamate receptor activity / Unblocking of NMDA receptors, glutamate binding and activation / AMPA glutamate receptor complex / Long-term potentiation / excitatory synapse / asymmetric synapse / glutamate-gated receptor activity ...Activation of AMPA receptors / postsynaptic endocytic zone / Trafficking of GluR2-containing AMPA receptors / AMPA glutamate receptor activity / Unblocking of NMDA receptors, glutamate binding and activation / AMPA glutamate receptor complex / Long-term potentiation / excitatory synapse / asymmetric synapse / glutamate-gated receptor activity / MECP2 regulates neuronal receptors and channels / ionotropic glutamate receptor signaling pathway / synaptic transmission, glutamatergic / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / postsynaptic density membrane / modulation of chemical synaptic transmission / endocytic vesicle membrane / amyloid-beta binding / postsynapse / chemical synaptic transmission / dendritic spine / postsynaptic density / external side of plasma membrane / neuronal cell body / dendrite / endoplasmic reticulum membrane / signal transduction / 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
ACETATE ION / GLUTAMIC ACID / Chem-RN8 / Glutamate receptor 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsTimm, D.E.
CitationJournal: Mol.Pharmacol. / Year: 2011
Title: Structural and functional analysis of two new positive allosteric modulators of GluA2 desensitization and deactivation.
Authors: Timm, D.E. / Benveniste, M. / Weeks, A.M. / Nisenbaum, E.S. / Partin, K.M.
History
DepositionApr 22, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 25, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 16, 2011Group: Database references
Revision 1.3Aug 23, 2017Group: Source and taxonomy / Category: entity_src_gen

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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
C: Glutamate receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,59616
Polymers92,7413
Non-polymers1,85613
Water15,853880
1
A: Glutamate receptor 2
C: Glutamate receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,7488
Polymers61,8272
Non-polymers9216
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Glutamate receptor 2
hetero molecules

B: Glutamate receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,69716
Polymers61,8272
Non-polymers1,87014
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Unit cell
Length a, b, c (Å)113.889, 163.232, 47.356
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, 3 molecules ABC

#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: 30913.506 Da / Num. of mol.: 3 / Fragment: UNP residues 413-527, 653-812
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GRIA2, GLUR2 / Production host: Escherichia coli (E. coli) / References: UniProt: P42262

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Non-polymers , 6 types, 893 molecules

#2: Chemical ChemComp-GLU / GLUTAMIC ACID


Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C5H9NO4
#3: Chemical ChemComp-RN8 / 3,3'-benzene-1,4-diylbis(4-cyano-5-ethylthiophene-2-carboxylic acid)


Mass: 436.503 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H16N2O4S2
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 880 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsR764G CONFLICT IN UNP ENTRY P42262

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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: 2.37 Å3/Da / Density % sol: 48.17 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG8000, Sodium Cacodylate, Zinc Acetate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 8, 2003
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. all: 97908 / Num. obs: 96319 / % possible obs: 98.5 % / Observed criterion σ(I): 2 / Redundancy: 6.2 % / Rmerge(I) obs: 0.055 / Net I/σ(I): 25.8
Reflection shellResolution: 1.7→1.76 Å / % possible all: 95.1

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Processing

Software
NameVersionClassification
HKL-2000data collection
X-PLORmodel building
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→40.96 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.938 / SU B: 2.013 / SU ML: 0.068 / Cross valid method: THROUGHOUT / ESU R Free: 0.109 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.22418 4820 5 %RANDOM
Rwork0.18915 ---
all0.19092 92922 --
obs0.19092 91417 98.38 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.884 Å2
Refinement stepCycle: LAST / Resolution: 1.7→40.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6062 0 108 880 7050
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0226352
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6141.9918566
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7595796
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.91724.458249
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.739151212
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0241530
X-RAY DIFFRACTIONr_chiral_restr0.1380.2940
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024653
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2030.23207
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3050.24443
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1650.2708
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.2390.26
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2370.280
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1840.238
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.0990.21
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2171.54009
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.82226259
X-RAY DIFFRACTIONr_scbond_it2.68832739
X-RAY DIFFRACTIONr_scangle_it4.1864.52296
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.746 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.318 337 -
Rwork0.258 6307 -
obs--93.51 %

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