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- PDB-2ojt: Structure and mechanism of kainate receptor modulation by anions -

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Basic information

Entry
Database: PDB / ID: 2ojt
TitleStructure and mechanism of kainate receptor modulation by anions
ComponentsGlutamate receptor, ionotropic kainate 1
KeywordsMEMBRANE PROTEIN
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
BROMIDE ION / Chem-UBA / Glutamate receptor ionotropic, kainate 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsMayer, M.L.
CitationJournal: Neuron / Year: 2007
Title: Structure and mechanism of kainate receptor modulation by anions.
Authors: Plested, A.J. / Mayer, M.L.
History
DepositionJan 14, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 3, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.3Aug 2, 2017Group: Source and taxonomy / Category: entity_src_gen
Revision 1.4Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / 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
Revision 1.5Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Remark 999 SEQUENCE THE FIRST TWO RESIDUES OF THE SEQUENCE ARE VECTOR ENCODED. GLUR5 RESIDUES 446-559 AND 682- ... SEQUENCE THE FIRST TWO RESIDUES OF THE SEQUENCE ARE VECTOR ENCODED. GLUR5 RESIDUES 446-559 AND 682-821 ARE LINKED VIA GLY-THR DIPEPTIDE. THE LAST RESIDUE OF THE SEQUENCE IS A MUTATION WHICH FACILITATED CRYSTALLIZATION.

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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)59,7668
Polymers58,4232
Non-polymers1,3436
Water5,188288
1
A: Glutamate receptor, ionotropic kainate 1
hetero molecules

A: Glutamate receptor, ionotropic kainate 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,7668
Polymers58,4232
Non-polymers1,3436
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_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)59,7668
Polymers58,4232
Non-polymers1,3436
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_455-x-1,y,-z+1/21
Unit cell
Length a, b, c (Å)97.598, 97.732, 128.688
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-301-

BR

21B-301-

BR

31A-526-

HOH

41B-521-

HOH

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Components

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


Mass: 29211.531 Da / Num. of mol.: 2 / Mutation: E821S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Tissue: Brain / Gene: Grik1, Glur5 / Plasmid: pET-22B (modified) / Production host: Escherichia coli (E. coli) / Strain (production host): Origami B(DE3) / References: UniProt: P22756
#2: Chemical ChemComp-BR / BROMIDE ION / Bromide


Mass: 79.904 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Br
#3: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400 / Polyethylene glycol


Mass: 238.278 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#4: Chemical ChemComp-UBA / (S)-1-(2-AMINO-2-CARBOXYETHYL)-3(2-CARBOXYTHIOPHENE-3-YL-METHYL)-5-METHYLPYRIMIDINE-2,4-DIONE


Mass: 353.350 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H15N3O6S
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 288 / 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: 2.63 Å3/Da / Density % sol: 53.15 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.7
Details: 19% PEG 1000, 120 mM Br, 100 mM Tris-HCl, pH 8.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.92017 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 21, 2006
RadiationMonochromator: Double crystal Si-220 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92017 Å / Relative weight: 1
ReflectionResolution: 1.95→30 Å / Num. obs: 44649 / % possible obs: 97.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 7.7 % / Biso Wilson estimate: 28.62 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 10.8
Reflection shellResolution: 1.95→2.03 Å / Redundancy: 7.6 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 3.8 / % possible all: 99

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2F34

2f34


Resolution: 1.95→27.83 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.936 / SU B: 6.139 / SU ML: 0.097 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.175 / ESU R Free: 0.158 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23291 2184 5 %RANDOM
Rwork0.1901 ---
all0.19223 41266 --
obs0.19223 41266 96.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 36.399 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å20 Å2
2--0.03 Å20 Å2
3----0.06 Å2
Refinement stepCycle: LAST / Resolution: 1.95→27.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4014 0 82 288 4384
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0224528
X-RAY DIFFRACTIONr_angle_refined_deg1.3311.9936138
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.845572
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.54424.316190
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.7515871
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.6881527
X-RAY DIFFRACTIONr_chiral_restr0.0970.2658
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023409
X-RAY DIFFRACTIONr_nbd_refined0.2250.32262
X-RAY DIFFRACTIONr_nbtor_refined0.3160.53248
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1990.5586
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2510.385
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2020.553
X-RAY DIFFRACTIONr_mcbond_it1.02222809
X-RAY DIFFRACTIONr_mcangle_it1.64934446
X-RAY DIFFRACTIONr_scbond_it1.04422006
X-RAY DIFFRACTIONr_scangle_it1.45531692
LS refinement shellResolution: 1.95→2 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.246 130 -
Rwork0.191 2676 -
obs--85.94 %
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)
10.20370.35930.33680.65130.70611.2709-0.11260.2446-0.05060.0207-0.02980.11350.14860.00950.14240.0657-0.0337-0.01610.0485-0.01130.0605-15.1743.65116.449
20.1799-0.7922-0.38513.90941.06691.76630.62450.2768-0.2994-0.0828-0.82640.40951.07190.82590.20180.10330.3699-0.23810.2895-0.21140.14849.607-11.9810.528
32.1914-2.85831.39883.7283-1.82450.8929-0.32510.1889-0.6075-1.1469-0.78250.5009-0.06340.84731.10750.3456-0.0961-0.12080.3246-0.19870.28146.337-14.90115.15
40.478-0.6909-0.61341.62690.45041.0901-0.08060.8-0.0597-0.0443-0.52120.38060.48020.573300.01030.1117-0.16760.2063-0.23390.21837.388-1.73411.814
50.11460.051-0.07050.56440.93041.7505-0.07270.4417-0.05560.0081-0.0601-0.096-0.25550.112900.0814-0.03990.03720.0368-0.02940.0767-10.8869.5785.57
60.61230.362-0.70840.2381-0.31331.28170.08740.13330.10050.0273-0.019-0.0603-0.0149-0.148200.0475-0.03190.01230.06680.01510.0547-44.856-15.07315.602
76.00960.24-1.55430.18560.62613.0925-0.83051.31420.67021.37550.3519-0.3342-1.1161-1.273200.33650.44250.31790.11780.3080.296-60.8769.86721.699
82.7095-1.32750.70593.8373-1.66170.72720.27020.52550.72870.1907-0.03190.1722-0.2840.097600.3588-0.05220.04990.36270.06790.3432-63.4846.58816.925
91.7844-0.6137-0.54410.70690.89411.17380.0960.69340.25340.53720.0643-0.1395-0.5603-0.421700.19430.11670.23-0.00550.17510.2132-50.347.22720.469
100.68290.075-0.94710.07830.04351.6240.03110.3457-0.09230.09050.0108-0.0512-0.1150.248800.0379-0.04360.02610.0847-0.03390.0758-39.168-11.02226.703
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 113
2X-RAY DIFFRACTION2A114 - 147
3X-RAY DIFFRACTION3A148 - 181
4X-RAY DIFFRACTION4A182 - 213
5X-RAY DIFFRACTION5A214 - 254
6X-RAY DIFFRACTION6B4 - 113
7X-RAY DIFFRACTION7B114 - 147
8X-RAY DIFFRACTION8B148 - 182
9X-RAY DIFFRACTION9B183 - 213
10X-RAY DIFFRACTION10B214 - 254

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