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- PDB-4mf3: Crystal Structure of Human GRIK1 complexed with a 6-(tetrazolyl)a... -

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Basic information

Entry
Database: PDB / ID: 4mf3
TitleCrystal Structure of Human GRIK1 complexed with a 6-(tetrazolyl)aryl decahydroisoquinoline antagonist
ComponentsGlutamate receptor ionotropic, kainate 1
KeywordsSIGNALING PROTEIN / Protein-Ligand Complex / Ligand Gated Ion Channel / Glutamate Receptor / Glutamate binding / none / Membrane
Function / homology
Function and homology information


Activation of Na-permeable kainate receptors / kainate selective glutamate receptor complex / glutamate receptor signaling pathway / Activation of Ca-permeable Kainate Receptor / kainate selective glutamate receptor activity / regulation of synaptic transmission, glutamatergic / synaptic transmission, glutamatergic / central nervous system development / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / postsynaptic density membrane ...Activation of Na-permeable kainate receptors / kainate selective glutamate receptor complex / glutamate receptor signaling pathway / Activation of Ca-permeable Kainate Receptor / kainate selective glutamate receptor activity / regulation of synaptic transmission, glutamatergic / synaptic transmission, glutamatergic / central nervous system development / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / postsynaptic density membrane / modulation of chemical synaptic transmission / presynaptic membrane / nervous system development / chemical synaptic transmission / intracellular membrane-bounded organelle / plasma membrane
Similarity search - Function
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 ...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-SXI / Glutamate receptor ionotropic, kainate 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsMartinez-Perez, J.A. / Iyengar, S. / Shannon, H.E. / Bleakman, D. / Alt, A. / Clawson, D.K. / Arnold, B.M. / Bell, M.G. / Bleisch, T.J. / Castano, A.M. ...Martinez-Perez, J.A. / Iyengar, S. / Shannon, H.E. / Bleakman, D. / Alt, A. / Clawson, D.K. / Arnold, B.M. / Bell, M.G. / Bleisch, T.J. / Castano, A.M. / Del Prado, M. / Dominguez, E. / Escribano, A.M. / Filla, S.A. / Ho, K.H. / Hudziak, K.J. / Jones, C.K. / Katofiasc, M.A. / Mateo, A. / Mathes, B.M. / Mattiuz, E.L. / Ogden, A.M.L. / Phebus, L.A. / Simmons, R.M.A. / Stack, D.R. / Stratford, R.E. / Winter, M.A. / Wu, Z. / Ornstein, P.L.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2013
Title: GluK1 antagonists from 6-(tetrazolyl)phenyl decahydroisoquinoline derivatives: in vitro profile and in vivo analgesic efficacy.
Authors: Martinez-Perez, J.A. / Iyengar, S. / Shannon, H.E. / Bleakman, D. / Alt, A. / Clawson, D.K. / Arnold, B.M. / Bell, M.G. / Bleisch, T.J. / Castano, A.M. / Del Prado, M. / Dominguez, E. / ...Authors: Martinez-Perez, J.A. / Iyengar, S. / Shannon, H.E. / Bleakman, D. / Alt, A. / Clawson, D.K. / Arnold, B.M. / Bell, M.G. / Bleisch, T.J. / Castano, A.M. / Del Prado, M. / Dominguez, E. / Escribano, A.M. / Filla, S.A. / Ho, K.H. / Hudziak, K.J. / Jones, C.K. / Mateo, A. / Mathes, B.M. / Mattiuz, E.L. / Ogden, A.M. / Simmons, R.M. / Stack, D.R. / Stratford, R.E. / Winter, M.A. / Wu, Z. / Ornstein, P.L.
History
DepositionAug 27, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 7, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 26, 2017Group: Source and taxonomy / Category: entity_src_gen
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glutamate receptor ionotropic, kainate 1
B: Glutamate receptor ionotropic, kainate 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,9744
Polymers59,2182
Non-polymers7562
Water23413
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2100 Å2
ΔGint-9 kcal/mol
Surface area24740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.018, 108.018, 109.766
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Glutamate receptor ionotropic, kainate 1 / GluK1 / Excitatory amino acid receptor 3 / EAA3 / Glutamate receptor 5 / GluR-5 / GluR5


Mass: 29608.959 Da / Num. of mol.: 2
Fragment: UNP residues 443-559 and 682-822, Extracellular domains
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GRIK1, GLUR5 / Production host: Escherichia coli (E. coli) / References: UniProt: P39086
#2: Chemical ChemComp-SXI / (3S,4aS,6S,8aR)-6-[3-chloro-2-(1H-tetrazol-5-yl)phenoxy]decahydroisoquinoline-3-carboxylic acid


Mass: 377.825 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H20ClN5O3 / Comment: antagonist*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / 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: 3.12 Å3/Da / Density % sol: 60.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8
Details: Protein mixed 1:1 with 55% MPD, 0.2M NH4H2PO4, 0.1M TRIS pH 8.0, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97929 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Feb 13, 2008
RadiationMonochromator: Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97929 Å / Relative weight: 1
ReflectionResolution: 2.52→46.8 Å / Num. all: 25146 / Num. obs: 24693 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 91.28 Å2
Reflection shellResolution: 2.52→2.65 Å / % possible all: 94

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Processing

Software
NameVersionClassificationNB
BUSTER-TNTrefinement
PDB_EXTRACT3.11data extraction
MAR345data collection
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
BUSTER2.11.5refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→20 Å / Cor.coef. Fo:Fc: 0.9182 / Cor.coef. Fo:Fc free: 0.8982 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2596 755 5.04 %RANDOM
Rwork0.2369 ---
all0.2381 15157 --
obs0.2381 14975 98.8 %-
Displacement parametersBiso max: 170.61 Å2 / Biso mean: 75.2778 Å2 / Biso min: 27.23 Å2
Baniso -1Baniso -2Baniso -3
1--1.3737 Å20 Å20 Å2
2---1.3737 Å20 Å2
3---2.7473 Å2
Refine analyzeLuzzati coordinate error obs: 0.506 Å
Refinement stepCycle: LAST / Resolution: 3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4059 0 52 13 4124
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONo_bond_d0.011495SINUSOIDAL2
X-RAY DIFFRACTIONo_angle_deg1.1102HARMONIC2
X-RAY DIFFRACTIONo_dihedral_angle_d3.57620HARMONIC5
X-RAY DIFFRACTIONt_it04198HARMONIC20
X-RAY DIFFRACTIONt_chiral_improper_torsion0560SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact04703SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d0.014198HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.15680HARMONIC2
X-RAY DIFFRACTIONt_omega_torsion3.57
X-RAY DIFFRACTIONt_other_torsion17.73
LS refinement shellResolution: 3→3.21 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.3421 161 6.03 %
Rwork0.2763 2510 -
all0.2802 2671 -
obs-3009 98.8 %

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