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- PDB-1vso: Crystal Structure of the Ligand-Binding Core of iGluR5 in Complex... -

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Basic information

Entry
Database: PDB / ID: 1vso
TitleCrystal Structure of the Ligand-Binding Core of iGluR5 in Complex With the Antagonist (S)-ATPO at 1.85 A resolution
ComponentsGlutamate receptor, ionotropic kainate 1
KeywordsMEMBRANE PROTEIN / Antagonist complex
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 / regulation of membrane potential / ionotropic glutamate receptor signaling pathway / 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-AT1 / Glutamate receptor ionotropic, kainate 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsHald, H. / Naur, P. / Gajhede, M. / Kastrup, J.S.
Citation
Journal: J.Biol.Chem. / Year: 2007
Title: Partial agonism and antagonism of the ionotropic glutamate receptor iGLuR5: structures of the ligand-binding core in complex with domoic acid and 2-amino-3-[5-tert-butyl-3-(phosphonomethoxy)-4- ...Title: Partial agonism and antagonism of the ionotropic glutamate receptor iGLuR5: structures of the ligand-binding core in complex with domoic acid and 2-amino-3-[5-tert-butyl-3-(phosphonomethoxy)-4-isoxazolyl]propionic acid.
Authors: Hald, H. / Naur, P. / Pickering, D.S. / Sprogoe, D. / Madsen, U. / Timmermann, D.B. / Ahring, P.K. / Liljefors, T. / Schousboe, A. / Egebjerg, J. / Gajhede, M. / Kastrup, J.S.
#1: Journal: FEBS Lett. / Year: 2005
Title: Crystal structure of the kainate receptor GluR5 ligand-binding core in complex with (S)-glutamate.
Authors: Naur, P. / Vestergaard, B. / Skov, L.K. / Egebjerg, J. / Gajhede, M. / Kastrup, J.S.
#2: Journal: J.Neurosci. / Year: 2006
Title: Crystal structures of the kainate receptor GluR5 ligand binding core dimer with novel GluR5-selective antagonists.
Authors: Mayer, M.L. / Ghosal, A. / Dolman, N.P. / Jane, D.E.
#3: Journal: J.Med.Chem. / Year: 2003
Title: Competitive antagonism of AMPA receptors by ligands of different classes: crystal structure of ATPO bound to the GluR2 ligand-binding core, in comparison with DNQX.
Authors: Hogner, A. / Greenwood, J.R. / Liljefors, T. / Lunn, M.L. / Egebjerg, J. / Larsen, I.K. / Gouaux, E. / Kastrup, J.S.
History
DepositionMar 29, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 3, 2007Provider: repository / Type: Initial release
Revision 1.1Oct 3, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Aug 2, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.4Oct 4, 2017Group: Refinement description / Category: software
Revision 1.5Aug 23, 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 / diffrn_source / 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 / _diffrn_source.pdbx_synchrotron_site / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999sequence There is a Ala -> Gly sequence conflict at residue 477 in the UniProt database.
Remark 300BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S) ...BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S). Authors state the functional receptor is a tetramer built of dimers-of-dimers. However, in the crystal only the dimer is present.

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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)29,5233
Polymers29,1081
Non-polymers4142
Water3,675204
1
A: Glutamate receptor, ionotropic kainate 1
hetero molecules

A: Glutamate receptor, ionotropic kainate 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,0466
Polymers58,2172
Non-polymers8294
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_655-x+1,-y,z1
Unit cell
Length a, b, c (Å)108.900, 108.900, 51.092
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number172
Space group name H-MP64
Components on special symmetry positions
IDModelComponents
11A-587-

HOH

21A-592-

HOH

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Components

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


Mass: 29108.453 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Grik1, Glur5 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): Origami 2 / References: UniProt: P22756
#2: Chemical ChemComp-AT1 / (S)-2-AMINO-3-(5-TERT-BUTYL-3-(PHOSPHONOMETHOXY)-4-ISOXAZOLYL)PROPIONIC ACID


Mass: 322.252 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H19N2O7P
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 204 / 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 Å3/Da / Density % sol: 59.05 %
Crystal growTemperature: 279 K / pH: 6.5
Details: 20% PEG 4000, 0.3 M lithium sulfate, 0.1 M cacodylate, VAPOR DIFFUSION, HANGING DROP, temperature 279K, pH 6.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.812
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jun 13, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.812 Å / Relative weight: 1
ReflectionResolution: 1.85→25 Å / Num. obs: 29461 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 4.8 % / Biso Wilson estimate: 21.9 Å2 / Rsym value: 0.059 / Net I/σ(I): 23.1
Reflection shellResolution: 1.85→1.92 Å / Mean I/σ(I) obs: 3.8 / Rsym value: 0.357 / % possible all: 99.9

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Phasing

Phasing MR
Highest resolutionLowest resolution
Rotation1.85 Å23.28 Å
Translation1.85 Å23.28 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
CNS1.1refinement
PDB_EXTRACT2data extraction
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1N0T, CHAIN A

1n0t


Resolution: 1.85→24.66 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 229797.41 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
Details: THE FULLY REFINED STRUCTURE COMPRISES THR433-GLN492, TRP498-LYS544, THE GLY-THR LINKER, PRO667-SER711 AND SER715-GLY803
RfactorNum. reflection% reflectionSelection details
Rfree0.231 1397 4.9 %RANDOM
Rwork0.202 ---
obs0.202 28456 96 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 48.9 Å2 / ksol: 0.41 e/Å3
Displacement parametersBiso mean: 24.7 Å2
Baniso -1Baniso -2Baniso -3
1--2.342 Å2-2.48 Å20 Å2
2---2.342 Å20 Å2
3---4.684 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.19 Å0.17 Å
Refinement stepCycle: LAST / Resolution: 1.85→24.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1933 0 27 204 2164
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.81
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.311.5
X-RAY DIFFRACTIONc_mcangle_it1.9862
X-RAY DIFFRACTIONc_scbond_it2.1022
X-RAY DIFFRACTIONc_scangle_it3.1822.5
LS refinement shellResolution: 1.85→1.93 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.276 165 5.2 %
Rwork0.267 2981 -
obs--85.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
X-RAY DIFFRACTION5ATO_PAR.TXTATO_TOP.TXT

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