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- PDB-3gba: X-ray structure of iGluR5 ligand-binding core (S1S2) in complex w... -

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Basic information

Entry
Database: PDB / ID: 3gba
TitleX-ray structure of iGluR5 ligand-binding core (S1S2) in complex with dysiherbaine at 1.35A resolution
ComponentsGlutamate receptor, ionotropic kainate 1
KeywordsMEMBRANE PROTEIN / ionotropic glutamate receptors / iGluR5 / ligand-binding core / agonist
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-DYH / Glutamate receptor ionotropic, kainate 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.35 Å
AuthorsFrydenvang, K. / Naur, P. / Gajhede, M. / Kastrup, J.S.
Citation
Journal: J.Biol.Chem. / Year: 2009
Title: Full Domain Closure of the Ligand-binding Core of the Ionotropic Glutamate Receptor iGluR5 Induced by the High Affinity Agonist Dysiherbaine and the Functional Antagonist 8,9-Dideoxyneodysiherbaine
Authors: Frydenvang, K. / Lash, L.L. / Naur, P. / Postila, P.A. / Pickering, D.S. / Smith, C.M. / Gajhede, M. / Sasaki, M. / Sakai, R. / Pentikainen, O.T. / Swanson, G.T. / 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.
History
DepositionFeb 19, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 17, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Aug 16, 2017Group: Data collection / Refinement description / Source and taxonomy
Category: diffrn_source / entity_src_gen / software / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Nov 1, 2023Group: 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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
D: Glutamate receptor, ionotropic kainate 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,19015
Polymers116,4344
Non-polymers1,75611
Water25,9601441
1
A: Glutamate receptor, ionotropic kainate 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,6365
Polymers29,1081
Non-polymers5284
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Glutamate receptor, ionotropic kainate 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,6365
Polymers29,1081
Non-polymers5284
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Glutamate receptor, ionotropic kainate 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5053
Polymers29,1081
Non-polymers3962
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Glutamate receptor, ionotropic kainate 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,4132
Polymers29,1081
Non-polymers3041
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.872, 66.902, 90.342
Angle α, β, γ (deg.)92.69, 94.66, 100.82
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 4 molecules ABCD

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


Mass: 29108.453 Da / Num. of mol.: 4 / Fragment: iGluR5 ligand-binding core (S1S2)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Glur5, Grik1 / Plasmid: pET-28a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): Origami 2 / References: UniProt: P22756

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Non-polymers , 5 types, 1452 molecules

#2: Chemical
ChemComp-DYH / (2R,3aR,6S,7R,7aR)-2-[(2S)-2-amino-2-carboxyethyl]-6-hydroxy-7-(methylamino)hexahydro-2H-furo[3,2-b]pyran-2-carboxylic acid


Mass: 304.296 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C12H20N2O7
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: 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
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1441 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsTHIS RESIDUE NUMBERING IS ISOFORM GLUR5-2 OF P22756 IN UNP. THE CONFLICT OF GLY 34 IS REFERED TO ...THIS RESIDUE NUMBERING IS ISOFORM GLUR5-2 OF P22756 IN UNP. THE CONFLICT OF GLY 34 IS REFERED TO ALA -> GLY SEQUENCE CONFLICT AT RESIDUE 462 IN UNP DATABASE.

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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: 2.28 Å3/Da / Density % sol: 45.95 %
Crystal growTemperature: 280 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: PEG8000, ammonium sulfate, phosphate-citrate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 280K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-2 / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Oct 5, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.35→89.862 Å / Num. all: 213789 / Num. obs: 213789 / % possible obs: 94.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 9.964 Å2 / Rmerge(I) obs: 0.079 / Rsym value: 0.079 / Net I/σ(I): 5.073
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.35-1.423.60.3421.7105516296990.34290.2
1.42-1.513.60.2352.4105003292640.23593.7
1.51-1.613.60.1613.899220276420.16194.4
1.61-1.743.60.1214.793194259570.12195.1
1.74-1.913.60.0946.586144240050.09495.8
1.91-2.133.60.0777.578549219460.07796.5
2.13-2.463.60.071869512194270.07197.3
2.46-3.023.60.067859028165330.06797.9
3.02-4.273.50.0599.244531127220.05997.6
4.27-31.453.40.0568.72224265940.05692.3

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å31.45 Å
Translation2.5 Å31.45 Å

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.2.13data scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.006data extraction
MAR345dtbdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ycj

1ycj


Resolution: 1.35→89.8 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.956 / WRfactor Rfree: 0.207 / WRfactor Rwork: 0.175 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.877 / SU B: 1.669 / SU ML: 0.032 / SU R Cruickshank DPI: 0.066 / SU Rfree: 0.058 / Isotropic thermal model: Restrained / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.065 / ESU R Free: 0.058 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.193 4297 2 %RANDOM
Rwork0.165 ---
obs0.165 209482 94.8 %-
all-213779 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 58.23 Å2 / Biso mean: 10.008 Å2 / Biso min: 2.99 Å2
Baniso -1Baniso -2Baniso -3
1--0.09 Å2-0.01 Å20.02 Å2
2--0.02 Å20.03 Å2
3---0.07 Å2
Refinement stepCycle: LAST / Resolution: 1.35→89.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8069 0 114 1441 9624
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0228631
X-RAY DIFFRACTIONr_bond_other_d0.0020.026021
X-RAY DIFFRACTIONr_angle_refined_deg1.1741.99411695
X-RAY DIFFRACTIONr_angle_other_deg0.8173.00314672
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.58951087
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.12324.306360
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.855151638
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.8191548
X-RAY DIFFRACTIONr_chiral_restr0.0720.21304
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.029379
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021677
X-RAY DIFFRACTIONr_nbd_refined0.2070.21538
X-RAY DIFFRACTIONr_nbd_other0.1820.26453
X-RAY DIFFRACTIONr_nbtor_refined0.180.24298
X-RAY DIFFRACTIONr_nbtor_other0.0860.24524
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.110.21060
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0270.21
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0820.219
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2310.276
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.10.273
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2171.56830
X-RAY DIFFRACTIONr_mcbond_other0.3731.52138
X-RAY DIFFRACTIONr_mcangle_it1.36928413
X-RAY DIFFRACTIONr_scbond_it2.08634092
X-RAY DIFFRACTIONr_scangle_it2.7964.53248
X-RAY DIFFRACTIONr_rigid_bond_restr1.087318222
X-RAY DIFFRACTIONr_sphericity_free3.36531443
X-RAY DIFFRACTIONr_sphericity_bonded2.112314459
LS refinement shellResolution: 1.35→1.39 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.238 279 -
Rwork0.202 14314 -
all-14593 -
obs-14314 87.19 %

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