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- PDB-6sbt: Structure of GluK1 ligand-binding domain (S1S2) in complex with N... -

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Entry
Database: PDB / ID: 6sbt
TitleStructure of GluK1 ligand-binding domain (S1S2) in complex with N-(7-(1H-imidazol-1-yl)-2,3-dioxo-6-(trifluoromethyl)-3,4-dihydroquinoxalin-1(2H)-yl benzamide at 2.3 A resolution
ComponentsGlutamate receptor ionotropic, kainate 1
KeywordsMEMBRANE PROTEIN / kainate receptor ligand-binding domain / GluK1-S1S2 / antagonist
Function / homology
Function and homology information


negative regulation of synaptic transmission, GABAergic / gamma-aminobutyric acid secretion / L-glutamate transmembrane transporter activity / amino acid transmembrane transport / positive regulation of gamma-aminobutyric acid secretion / Activation of Na-permeable kainate receptors / kainate selective glutamate receptor complex / Activation of Ca-permeable Kainate Receptor / negative regulation of synaptic transmission, glutamatergic / regulation of short-term neuronal synaptic plasticity ...negative regulation of synaptic transmission, GABAergic / gamma-aminobutyric acid secretion / L-glutamate transmembrane transporter activity / amino acid transmembrane transport / positive regulation of gamma-aminobutyric acid secretion / Activation of Na-permeable kainate receptors / kainate selective glutamate receptor complex / Activation of Ca-permeable Kainate Receptor / negative regulation of synaptic transmission, glutamatergic / regulation of short-term neuronal synaptic plasticity / inhibitory postsynaptic potential / synaptic transmission, GABAergic / glutamate binding / adult behavior / behavioral response to pain / modulation of excitatory postsynaptic potential / extracellularly glutamate-gated ion channel activity / membrane depolarization / kainate selective glutamate receptor activity / ionotropic glutamate receptor complex / sodium ion transmembrane transport / glutamate-gated receptor activity / glutamate-gated calcium ion channel activity / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / potassium ion transmembrane transport / presynaptic modulation of chemical synaptic transmission / ionotropic glutamate receptor signaling pathway / regulation of membrane potential / SNARE binding / excitatory postsynaptic potential / synaptic transmission, glutamatergic / establishment of localization in cell / positive regulation of synaptic transmission, GABAergic / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / postsynaptic density membrane / modulation of chemical synaptic transmission / regulation of synaptic plasticity / terminal bouton / presynaptic membrane / nervous system development / scaffold protein binding / chemical synaptic transmission / postsynaptic membrane / postsynaptic density / receptor complex / neuronal cell body / glutamatergic synapse / dendrite / synapse / 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
Chem-L5H / Glutamate receptor ionotropic, kainate 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsMoellerud, S. / Frydenvang, K. / Kastrup, J.S.
CitationJournal: Acs Chem Neurosci / Year: 2019
Title: N-(7-(1H-Imidazol-1-yl)-2,3-dioxo-6-(trifluoromethyl)-3,4-dihydroquinoxalin-1(2H)-yl)benzamide, a New Kainate Receptor Selective Antagonist and Analgesic: Synthesis, X-ray Crystallography, ...Title: N-(7-(1H-Imidazol-1-yl)-2,3-dioxo-6-(trifluoromethyl)-3,4-dihydroquinoxalin-1(2H)-yl)benzamide, a New Kainate Receptor Selective Antagonist and Analgesic: Synthesis, X-ray Crystallography, Structure-Affinity Relationships, and in Vitro and in Vivo Pharmacology.
Authors: Mollerud, S. / Hansen, R.B. / Pallesen, J. / Temperini, P. / Pasini, D. / Bornholt, J. / Nielsen, B. / Mamedova, E. / Chalupnik, P. / Paternain, A.V. / Lerma, J. / Diaz-delCastillo, M. / ...Authors: Mollerud, S. / Hansen, R.B. / Pallesen, J. / Temperini, P. / Pasini, D. / Bornholt, J. / Nielsen, B. / Mamedova, E. / Chalupnik, P. / Paternain, A.V. / Lerma, J. / Diaz-delCastillo, M. / Andreasen, J.T. / Frydenvang, K. / Kastrup, J.S. / Johansen, T.N. / Pickering, D.S.
History
DepositionJul 22, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 30, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Nov 27, 2019Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 24, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)29,9718
Polymers29,1081
Non-polymers8637
Water1,08160
1
A: Glutamate receptor ionotropic, kainate 1
hetero molecules

A: Glutamate receptor ionotropic, kainate 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,94216
Polymers58,2172
Non-polymers1,72514
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation17_555x-y+1/3,-y+2/3,-z+2/31
Buried area4570 Å2
ΔGint-100 kcal/mol
Surface area23420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.275, 89.275, 156.321
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-305-

CL

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Glutamate receptor ionotropic, kainate 1 / GluK1 / Glutamate receptor 5 / GluR5


Mass: 29108.453 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Native GluK1 is a membrane protein. the protein crystallized is the extracellular ligand-binding domain of GluK1. Transmembrane regions were genetically removed and replaced with a Gly-Thr ...Details: Native GluK1 is a membrane protein. the protein crystallized is the extracellular ligand-binding domain of GluK1. Transmembrane regions were genetically removed and replaced with a Gly-Thr linker (residue 117-118). The sequence matches discontinuously with reference database (430-544,667-805). Gly is a cloning remnance.,Native GluK1 is a membrane protein. the protein crystallized is the extracellular ligand-binding domain of GluK1. Transmembrane regions were genetically removed and replaced with a Gly-Thr linker (residue 117-118). The sequence matches discontinuously with reference database (430-544,667-805). Gly is a cloning remnance. There is a sequence conflict at residue 34 (462) of the crystallized protein due to differences in database sequence (see genebank accesion no.AAA02874). The database sequence is P22756-2, isoform GluR5-2.
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Grik1, Glur5 / Plasmid: pET28a+ / Production host: Escherichia coli (E. coli) / Strain (production host): Origami 2 / References: UniProt: P22756

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Non-polymers , 5 types, 67 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-L5H / ~{N}-[7-imidazol-1-yl-2,3-bis(oxidanylidene)-6-(trifluoromethyl)-4~{H}-quinoxalin-1-yl]benzamide


Mass: 415.325 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H12F3N5O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 60 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.06 Å3/Da / Density % sol: 40.27 %
Crystal growTemperature: 279 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 20% PEG4000, 0.3M lithiumsulfate, 0.1M phoshat-citate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.07227 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 5, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07227 Å / Relative weight: 1
ReflectionResolution: 2.3→44.6375 Å / Num. obs: 10935 / % possible obs: 100 % / Redundancy: 13.3 % / Biso Wilson estimate: 27.117 Å2 / Rpim(I) all: 0.031 / Rrim(I) all: 0.116 / Rsym value: 0.111 / Net I/av σ(I): 6.2 / Net I/σ(I): 17.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRpim(I) allRrim(I) allRsym value% possible all
2.3-2.4212.80.4961.515750.1430.5160.496100
2.42-2.5713.50.4131.814880.1160.4290.413100
2.57-2.7513.80.3042.514010.0850.3160.304100
2.75-2.9713.60.2093.513080.0590.2180.209100
2.97-3.2512.70.1375.312060.040.1430.137100
3.25-3.64140.097.811000.0250.0940.09100
3.64-4.213.50.068109700.0190.0710.068100
4.2-5.1412.80.05512.28390.0160.0570.055100
5.14-7.2713.30.06310.96610.0180.0660.063100
7.27-44.637511.90.04212.83870.0120.0440.04299.6

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Processing

Software
NameVersionClassification
SCALA3.3.20data scaling
PHENIXrefinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4QF9

4qf9


Resolution: 2.3→44.6375 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.79 / Phase error: 25.22
RfactorNum. reflection% reflection
Rfree0.2485 524 4.79 %
Rwork0.2053 --
obs0.2073 10934 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 138.77 Å2 / Biso mean: 49.5859 Å2 / Biso min: 2.13 Å2
Refinement stepCycle: final / Resolution: 2.3→44.6375 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1995 0 82 61 2138
Biso mean--67.06 35.59 -
Num. residues----249
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022110
X-RAY DIFFRACTIONf_angle_d0.5742849
X-RAY DIFFRACTIONf_chiral_restr0.041308
X-RAY DIFFRACTIONf_plane_restr0.003352
X-RAY DIFFRACTIONf_dihedral_angle_d12.161255
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.3001-2.53150.3031250.23162571
2.5315-2.89780.30021440.23552547
2.8978-3.65060.24241400.20522589
3.6506-44.63750.21331150.18752703
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.1309-0.0259-0.05784.0297-0.1392.8527-0.1070.5755-0.3564-0.3161-0.0048-0.13750.53950.06720.0530.37450.01750.01940.2308-0.07230.18830.515912.245431.9544
21.59761.00750.66642.3724-0.57191.938-0.02150.06820.0876-0.0224-0.065-0.0201-0.0733-0.01740.07890.25010.01040.01320.16710.01620.184-1.665627.464237.9415
32.6379-2.5511-0.78384.8634-1.44162.397-0.2666-0.8360.94890.70360.21-1.1871-1.03440.52720.94610.7115-0.4916-0.4791.28420.57491.159430.266434.636847.5558
45.56292.7833-2.68169.1592-2.37795.2635-0.1081-0.1072-0.1791-0.0125-0.1947-0.68280.03640.25030.26380.4802-0.07420.00380.19080.04690.36218.637440.840639.1178
53.30822.7894-1.91492.3609-1.6811.17290.23980.3971-0.291-1.384-0.749-1.27150.19480.73310.30220.73190.11620.38310.49570.28050.864322.462926.790136.8246
64.26560.1517-0.03243.838-2.07872.72830.0422-0.14760.00270.1407-0.3233-0.39460.26270.29510.15390.27310.03870.02010.18320.01880.16594.752521.065646.5929
72.0147-0.469-1.72032.79330.03414.1088-0.3162-0.5567-0.38280.6198-0.3678-0.24340.35490.37080.56720.35750.2261-0.01930.36650.09240.297110.345211.153844.5356
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 47 )A4 - 47
2X-RAY DIFFRACTION2chain 'A' and (resid 48 through 115 )A48 - 115
3X-RAY DIFFRACTION3chain 'A' and (resid 116 through 132 )A116 - 132
4X-RAY DIFFRACTION4chain 'A' and (resid 133 through 172 )A133 - 172
5X-RAY DIFFRACTION5chain 'A' and (resid 173 through 198 )A173 - 198
6X-RAY DIFFRACTION6chain 'A' and (resid 199 through 239 )A199 - 239
7X-RAY DIFFRACTION7chain 'A' and (resid 240 through 252 )A240 - 252

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