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

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Basic information

Entry
Database: PDB / ID: 3gbb
TitleX-ray structure of iGluR5 ligand-binding core (S1S2) in complex with MSVIII-19 at 2.10A resolution
ComponentsGlutamate receptor, ionotropic kainate 1
KeywordsMEMBRANE PROTEIN / ionotropic glutamate receptors / iGluR5 / ligand-binding core / weak 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 / 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-MS8 / Glutamate receptor ionotropic, kainate 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 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: 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, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Sep 9, 2020Group: Database references / Derived calculations / Structure summary
Category: struct / struct_ref_seq_dif / struct_site
Item: _struct.title / _struct_ref_seq_dif.details ..._struct.title / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 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
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
B: Glutamate receptor, ionotropic kainate 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,7354
Polymers58,2172
Non-polymers5192
Water6,233346
1
A: Glutamate receptor, ionotropic kainate 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3682
Polymers29,1081
Non-polymers2591
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)29,3682
Polymers29,1081
Non-polymers2591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.900, 45.120, 66.980
Angle α, β, γ (deg.)100.890, 92.310, 94.650
Int Tables number1
Space group name H-MP1

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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.: 2 / 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
#2: Chemical ChemComp-MS8 / (2R,3aR,7aR)-2-[(2S)-2-amino-3-hydroxy-3-oxo-propyl]-3,3a,5,6,7,7a-hexahydrofuro[4,5-b]pyran-2-carboxylic acid


Mass: 259.256 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H17NO6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 346 / Source method: isolated from a natural source / Formula: H2O
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: 46 %
Crystal growTemperature: 280 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: PEG4000, LiSO4, 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: 1.043 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: May 26, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.043 Å / Relative weight: 1
ReflectionResolution: 2.1→65.668 Å / Num. all: 28932 / Num. obs: 28932 / % possible obs: 96.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.2 % / Biso Wilson estimate: 12.2 Å2 / Rmerge(I) obs: 0.081 / Rsym value: 0.081 / Net I/σ(I): 8.511
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.271 / Mean I/σ(I) obs: 2.8 / Num. measured all: 9087 / Num. unique all: 4160 / Rsym value: 0.271 / % possible all: 94.5

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å65.67 Å
Translation2.5 Å65.67 Å

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Processing

Software
NameVersionClassificationNB
SCALA3.2.19data scaling
PHASERphasing
CNSrefinement
PDB_EXTRACT3.006data extraction
MAR345dtbdata collection
xia2data reduction
xia2data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1YCJ

1ycj


Resolution: 2.1→29.28 Å / Rfactor Rfree error: 0.007 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.828 / Data cutoff high absF: 863358.99 / Data cutoff low absF: 0 / Isotropic thermal model: restrained / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.251 1452 5 %Random
Rwork0.201 ---
all-28925 --
obs-28925 96.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 55.45 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso max: 70.26 Å2 / Biso mean: 23.3 Å2 / Biso min: 2.08 Å2
Baniso -1Baniso -2Baniso -3
1-6.28 Å20.43 Å2-7.2 Å2
2---6.77 Å2-0.38 Å2
3---0.49 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.32 Å0.24 Å
Refinement stepCycle: LAST / Resolution: 2.1→29.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4123 0 36 346 4505
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.243
X-RAY DIFFRACTIONc_mcbond_it1.4211.5
X-RAY DIFFRACTIONc_scbond_it2.1742
X-RAY DIFFRACTIONc_mcangle_it2.2932
X-RAY DIFFRACTIONc_scangle_it3.2152.5
X-RAY DIFFRACTIONc_dihedral_angle_d22
X-RAY DIFFRACTIONc_improper_angle_d0.98
LS refinement shellResolution: 2.1→2.12 Å / Rfactor Rfree error: 0.045
RfactorNum. reflection% reflection
Rfree0.303 45 4.7 %
Rwork0.276 913 -
obs-4495 90 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3lig_prodrg.paramlig_prodrg.top

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