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- PDB-6fz4: Structure of GluK1 ligand-binding domain in complex with N-(7-flu... -

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Basic information

Entry
Database: PDB / ID: 6fz4
TitleStructure of GluK1 ligand-binding domain in complex with N-(7-fluoro-2,3-dioxo-6-(trifluoromethyl)-3,4-dihydroquinoxalin-1(2H)-yl)-2-hydroxybenzamide at 1.85 A resolution
ComponentsGlutamate receptor ionotropic, kainate 1,Glutamate receptor ionotropic, kainate 1
KeywordsMEMBRANE PROTEIN / Kainate receptor ligand-binding domain / GluK1-S1S2
Function / homology
Function and homology information


gamma-aminobutyric acid secretion / negative regulation of synaptic transmission, GABAergic / L-glutamate transmembrane transporter activity / 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 ...gamma-aminobutyric acid secretion / negative regulation of synaptic transmission, GABAergic / L-glutamate transmembrane transporter activity / 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 / membrane depolarization / kainate selective glutamate receptor activity / ionotropic glutamate receptor complex / extracellularly glutamate-gated ion channel activity / glutamate-gated receptor activity / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / presynaptic modulation of chemical synaptic transmission / ionotropic glutamate receptor signaling pathway / excitatory postsynaptic potential / SNARE binding / synaptic transmission, glutamatergic / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / establishment of localization in cell / regulation of membrane potential / positive regulation of synaptic transmission, GABAergic / 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 density / receptor complex / neuronal cell body / glutamatergic synapse / synapse / dendrite / identical protein binding / membrane / 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-EC8 / Glutamate receptor ionotropic, kainate 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.85 Å
AuthorsKastrup, J.S. / Frydenvang, K. / Mollerud, S.
CitationJournal: Acs Chem Neurosci / Year: 2019
Title: N1-Substituted Quinoxaline-2,3-diones as Kainate Receptor Antagonists: X-ray Crystallography, Structure-Affinity Relationships, and in Vitro Pharmacology.
Authors: Pallesen, J. / Mollerud, S. / Frydenvang, K. / Pickering, D.S. / Bornholdt, J. / Nielsen, B. / Pasini, D. / Han, L. / Marconi, L. / Kastrup, J.S. / Johansen, T.N.
History
DepositionMar 14, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 23, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name
Revision 1.2Jan 17, 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,Glutamate receptor ionotropic, kainate 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,0849
Polymers29,1081
Non-polymers9758
Water1,964109
1
A: Glutamate receptor ionotropic, kainate 1,Glutamate receptor ionotropic, kainate 1
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)60,16718
Polymers58,2172
Non-polymers1,95016
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556y,x,-z+11
Buried area6080 Å2
ΔGint-93 kcal/mol
Surface area23430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.867, 88.867, 157.145
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 29108.453 Da / Num. of mol.: 1
Fragment: UNP residues 430-544,UNP residues 667-805,UNP residues 430-544,UNP residues 667-805
Source method: isolated from a genetically manipulated source
Details: THE DATABASE SEQUENCE IS P22756-2, ISOFORM GLUR5-2. THE PROTEIN CRYSTALLIZED IS THE EXTRACELLULAR LIGAND-BINDING DOMAIN OF GLUK1. TRANSMEMBRANE REGIONS WERE REPLACED WITH A GLY-THR LINKER ...Details: THE DATABASE SEQUENCE IS P22756-2, ISOFORM GLUR5-2. THE PROTEIN CRYSTALLIZED IS THE EXTRACELLULAR LIGAND-BINDING DOMAIN OF GLUK1. TRANSMEMBRANE REGIONS WERE REPLACED WITH A GLY-THR LINKER (RESIDUES 117-118). THE SEQUENCE MATCHES DISCONTINOUSLY WITH REFERENCE DATABASE (430-544, 667-805). THERE IS A SEQUENCE CONFLICT AT RESIDUE 34 (462) OF THE CRYSTALLIZED PROTEIN DUE TO DIFFERENCES IN DATABASE SEQUENCE (SEE GENBANK ACCESION NO.AAA02874). GLY1 IS A CLONING REMNANT.,THE DATABASE SEQUENCE IS P22756-2, ISOFORM GLUR5-2. THE PROTEIN CRYSTALLIZED IS THE EXTRACELLULAR LIGAND-BINDING DOMAIN OF GLUK1. TRANSMEMBRANE REGIONS WERE REPLACED WITH A GLY-THR LINKER (RESIDUES 117-118). THE SEQUENCE MATCHES DISCONTINOUSLY WITH REFERENCE DATABASE (430-544, 667-805). THERE IS A SEQUENCE CONFLICT AT RESIDUE 34 (462) OF THE CRYSTALLIZED PROTEIN DUE TO DIFFERENCES IN DATABASE SEQUENCE (SEE GENBANK ACCESION NO.AAA02874). GLY1 IS A CLONING REMNANT.
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Grik1, Glur5 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Origami 2 / References: UniProt: P22756

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Non-polymers , 5 types, 117 molecules

#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-EC8 / N-(7-fluoro-2,3-dioxo-6-(trifluoromethyl)-3,4-dihydroquinoxalin-1(2H)-yl)-2-hydroxybenzamide


Mass: 383.254 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H9F4N3O4
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 109 / 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: 2.05 Å3/Da / Density % sol: 40.04 %
Crystal growTemperature: 280 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 20% PEG4000, 0.1M lithium sulfate, 0.1M sodium acetate pH 5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 2, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.85→69.117 Å / Num. obs: 20684 / % possible obs: 100 % / Redundancy: 10 % / Biso Wilson estimate: 23.06 Å2 / Rpim(I) all: 0.027 / Rrim(I) all: 0.086 / Rsym value: 0.081 / Net I/av σ(I): 6.1 / Net I/σ(I): 15.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRpim(I) allRrim(I) allRsym value% possible all
1.85-1.959.60.4411.629710.150.4660.441100
1.95-2.079.90.2632.628270.0880.2780.263100
2.07-2.2110.40.1773.926600.0580.1860.177100
2.21-2.3910.20.1365.124730.0450.1430.136100
2.39-2.629.60.1086.323060.0370.1140.108100
2.62-2.9310.50.097.320680.0290.0950.09100
2.93-3.3810.20.0768.318460.0250.080.076100
3.38-4.149.60.0639.715690.0210.0670.063100
4.14-5.8510.10.05311.312460.0180.0560.053100
5.85-37.3769.20.04911.67180.0170.0520.04999.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.12 Å37.38 Å
Translation3.12 Å37.38 Å

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Processing

Software
NameVersionClassification
SCALA3.3.20data scaling
PHASER2.5.1phasing
PHENIXrefinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4qf9

4qf9


Resolution: 1.85→37.376 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 20.74
RfactorNum. reflection% reflection
Rfree0.2164 1058 5.12 %
Rwork0.1865 --
obs0.188 20681 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 110.77 Å2 / Biso mean: 33.0856 Å2 / Biso min: 10.47 Å2
Refinement stepCycle: final / Resolution: 1.85→37.376 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1999 0 63 110 2172
Biso mean--52.09 33.31 -
Num. residues----250
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0132322
X-RAY DIFFRACTIONf_angle_d1.133138
X-RAY DIFFRACTIONf_chiral_restr0.059341
X-RAY DIFFRACTIONf_plane_restr0.008390
X-RAY DIFFRACTIONf_dihedral_angle_d13.5431390
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.8501-1.93430.2581240.225324222546
1.9343-2.03620.24451140.207424352549
2.0362-2.16380.2221430.193824222565
2.1638-2.33090.22831280.194724172545
2.3309-2.56540.25931510.203224302581
2.5654-2.93650.26131290.193424542583
2.9365-3.69910.21551420.169724662608
3.6991-37.38390.16911270.176325772704
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)
12.4438-1.2316-0.18322.81760.11292.2387-0.00840.2859-0.2475-0.0829-0.09920.28380.0887-0.13820.00590.11170.00040.01040.1783-0.05640.122318.779835.16463.4601
21.59260.32470.1711.89880.52671.68860.16440.3308-0.29960.0796-0.26140.25830.26680.00630.11070.2450.0598-0.00380.4056-0.2010.360516.388314.984563.46
32.842-0.1523-0.47822.86060.13981.8057-0.18020.1606-0.20790.21180.08180.32990.0917-0.40130.08350.1484-0.00770.02260.2853-0.04350.146312.906137.08172.8188
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 151 )A4 - 151
2X-RAY DIFFRACTION2chain 'A' and (resid 152 through 200 )A152 - 200
3X-RAY DIFFRACTION3chain 'A' and (resid 201 through 253 )A201 - 253

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