[English] 日本語
Yorodumi
- PDB-6sbt: Structure of GluK1 ligand-binding domain (S1S2) in complex with N... -

+
Open data


ID or keywords:

Loading...

-
Basic information

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 / modulation of excitatory postsynaptic potential / behavioral response to pain / membrane depolarization / kainate selective glutamate receptor activity / ionotropic glutamate receptor complex / extracellularly glutamate-gated ion channel activity / 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 / positive regulation of synaptic transmission, GABAergic / establishment of localization in cell / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
Components

-
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

-
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

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more