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- PDB-4qf9: Structure of GluK1 ligand-binding domain (S1S2) in complex with (... -

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Basic information

Entry
Database: PDB / ID: 4qf9
TitleStructure of GluK1 ligand-binding domain (S1S2) in complex with (S)-2-amino-4-(2,3-dioxo-1,2,3,4-tetrahydroquinoxalin-6-yl)butanoic acid at 2.28 A resolution
ComponentsGlutamate receptor ionotropic, kainate 1
KeywordsMEMBRANE PROTEIN / Kainate receptor ligand-binding domain / GluK1-S1S2 / antagonist
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 / 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 / glutamate-gated receptor activity / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / excitatory postsynaptic potential / presynaptic modulation of chemical synaptic transmission / ionotropic glutamate receptor signaling pathway / regulation of membrane potential / SNARE binding / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / synaptic transmission, glutamatergic / establishment of localization in cell / positive regulation of synaptic transmission, GABAergic / postsynaptic density membrane / regulation of synaptic plasticity / modulation of chemical synaptic transmission / terminal bouton / presynaptic membrane / nervous system development / chemical synaptic transmission / scaffold protein binding / postsynaptic density / receptor complex / dendrite / neuronal cell body / glutamatergic synapse / synapse / membrane / identical protein binding / 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-35K / ACETATE ION / Glutamate receptor ionotropic, kainate 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.28 Å
AuthorsKristensen, C.M. / Frydenvang, K. / Kastrup, J.S.
CitationJournal: ACS Chem Neurosci / Year: 2015
Title: Binding Mode of an alpha-Amino Acid-Linked Quinoxaline-2,3-dione Analogue at Glutamate Receptor Subtype GluK1.
Authors: Demmer, C.S. / Moller, C. / Brown, P.M. / Han, L. / Pickering, D.S. / Nielsen, B. / Bowie, D. / Frydenvang, K. / Kastrup, J.S. / Bunch, L.
History
DepositionMay 20, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 22, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 1, 2015Group: Data collection / Database references
Revision 1.2Jul 26, 2017Group: Data collection / Source and taxonomy / Category: diffrn_source / entity_src_gen / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Aug 9, 2017Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.4Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
C: Glutamate receptor ionotropic, kainate 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,25917
Polymers87,3253
Non-polymers1,93314
Water4,324240
1
A: Glutamate receptor ionotropic, kainate 1
C: Glutamate receptor ionotropic, kainate 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,2249
Polymers58,2172
Non-polymers1,0077
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Glutamate receptor ionotropic, kainate 1
hetero molecules

B: Glutamate receptor ionotropic, kainate 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,06916
Polymers58,2172
Non-polymers1,85214
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Unit cell
Length a, b, c (Å)117.265, 86.802, 78.282
Angle α, β, γ (deg.)90.000, 111.620, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-304-

CL

21B-307-

PG4

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Components

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Protein , 1 types, 3 molecules ABC

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


Mass: 29108.453 Da / Num. of mol.: 3 / Fragment: UNP residues 445-559, 682-820
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Strain: RAT / Gene: Glur5, Grik1 / Plasmid: pET28a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): Origami 2 / References: UniProt: P22756

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Non-polymers , 7 types, 254 molecules

#2: Chemical ChemComp-35K / (2S)-2-amino-4-(2,3-dioxo-1,2,3,4-tetrahydroquinoxalin-6-yl)butanoic acid


Mass: 263.249 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C12H13N3O4
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


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


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 240 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsThe protein crystallized is the extracellular ligand-binding domain of GluK1. Transmembrane regions ...The protein crystallized is the extracellular ligand-binding domain of GluK1. Transmembrane regions were genetically removed and replaced with a Gly-Thr linker

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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: 2.12 Å3/Da / Density % sol: 42 %
Crystal growTemperature: 279 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 24.4% PEG4000, 0.3M ammonium sulfate, 0.1M phosphate citrate buffer pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 279K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 11, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.28→29.39 Å / Num. all: 33230 / Num. obs: 33230 / % possible obs: 99.7 % / Redundancy: 4 % / Biso Wilson estimate: 37 Å2 / Rsym value: 0.094 / Net I/σ(I): 8.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.28-2.440.3771.91905547890.37799.3
2.4-2.5540.252.91822645760.2599.5
2.55-2.7340.18241714043070.18299.6
2.73-2.9440.1295.51584739780.12999.7
2.94-3.2240.0937.41472236940.09399.8
3.22-3.640.0778.61339733670.07799.9
3.6-4.163.90.1174.21154429570.117100
4.16-5.140.04713.51001425260.047100
5.1-7.213.90.04810.7770919590.048100
7.21-29.3893.80.0368.2410710770.03698.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 42.7 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å29.39 Å
Translation2.5 Å29.39 Å

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Processing

Software
NameVersionClassificationNB
SCALA3.3.16data scaling
PHASER2.1.4phasing
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.14data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1VSO MOL A

1vso


Resolution: 2.28→29.389 Å / FOM work R set: 0.8166 / SU ML: 0.28 / Isotropic thermal model: isotropic B individual / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 25.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2465 1683 5.07 %RANDOM
Rwork0.1975 ---
obs0.2 33201 99.51 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 92.25 Å2 / Biso mean: 39.64 Å2 / Biso min: 17.67 Å2
Refinement stepCycle: LAST / Resolution: 2.28→29.389 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5955 0 126 240 6321
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026234
X-RAY DIFFRACTIONf_angle_d0.6378403
X-RAY DIFFRACTIONf_chiral_restr0.043921
X-RAY DIFFRACTIONf_plane_restr0.0041043
X-RAY DIFFRACTIONf_dihedral_angle_d12.8182365
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection allNum. reflection obs% reflection obs (%)
2.28-2.34710.28471450.223426072752260799
2.3471-2.42280.29211150.214226152730261599
2.4228-2.50940.32071260.220926132739261399
2.5094-2.60980.26191420.212126272769262799
2.6098-2.72850.31351520.213225872739258799
2.7285-2.87220.30361270.2243263327602633100
2.8722-3.0520.26851600.2105258027402580100
3.052-3.28740.22541460.2025263727832637100
3.2874-3.61760.29511270.1962265627832656100
3.6176-4.13990.22631330.212826152748261599
4.1399-5.21110.15811610.1547265928202659100
5.2111-29.39120.25461490.1783268928382689100

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