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- PDB-2i0b: Crystal structure of the GluR6 ligand binding core ELKQ mutant di... -

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Basic information

Entry
Database: PDB / ID: 2i0b
TitleCrystal structure of the GluR6 ligand binding core ELKQ mutant dimer at 1.96 Angstroms Resolution
ComponentsGlutamate receptor, ionotropic kainate 2
KeywordsMEMBRANE PROTEIN
Function / homology
Function and homology information


mossy fiber rosette / detection of cold stimulus involved in thermoception / 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 / glutamate receptor activity / ubiquitin conjugating enzyme binding ...mossy fiber rosette / detection of cold stimulus involved in thermoception / 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 / glutamate receptor activity / ubiquitin conjugating enzyme binding / receptor clustering / modulation of excitatory postsynaptic potential / regulation of JNK cascade / kainate selective glutamate receptor activity / ionotropic glutamate receptor complex / extracellularly glutamate-gated ion channel activity / neuronal action potential / behavioral fear response / positive regulation of synaptic transmission / glutamate-gated receptor activity / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / presynaptic modulation of chemical synaptic transmission / excitatory postsynaptic potential / dendrite cytoplasm / hippocampal mossy fiber to CA3 synapse / SNARE binding / synaptic transmission, glutamatergic / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / PDZ domain binding / regulation of membrane potential / postsynaptic density membrane / regulation of long-term neuronal synaptic plasticity / modulation of chemical synaptic transmission / terminal bouton / intracellular calcium ion homeostasis / positive regulation of neuron apoptotic process / presynaptic membrane / scaffold protein binding / chemical synaptic transmission / postsynaptic membrane / perikaryon / neuron apoptotic process / negative regulation of neuron apoptotic process / postsynaptic density / axon / neuronal cell body / glutamatergic synapse / ubiquitin protein ligase binding / 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
GLUTAMIC ACID / Glutamate receptor ionotropic, kainate 2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 Å
AuthorsMayer, M.L.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2006
Title: Conformational restriction blocks glutamate receptor desensitization.
Authors: Weston, M.C. / Schuck, P. / Ghosal, A. / Rosenmund, C. / Mayer, M.L.
History
DepositionAug 10, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 21, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Aug 16, 2017Group: Source and taxonomy / Category: entity_src_gen
Revision 1.4Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.5Oct 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 1.6Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Remark 300BIOMOLECULE: 1, 2 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN BIOLOGICALLY ...BIOMOLECULE: 1, 2 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. AUTHOR STATES: DIMERS FORMED BY CHAINS B AND C, ARE BELIEVED TO OCCUR IN THE INTACT MEMBRANE PROTEIN.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glutamate receptor, ionotropic kainate 2
B: Glutamate receptor, ionotropic kainate 2
C: Glutamate receptor, ionotropic kainate 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,6527
Polymers88,1153
Non-polymers5374
Water9,692538
1
A: Glutamate receptor, ionotropic kainate 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5192
Polymers29,3721
Non-polymers1471
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Glutamate receptor, ionotropic kainate 2
C: Glutamate receptor, ionotropic kainate 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,1345
Polymers58,7432
Non-polymers3903
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2220 Å2
ΔGint-27 kcal/mol
Surface area23060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.215, 94.215, 219.836
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
DetailsChains B and C form a biologically relevant dimer

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Components

#1: Protein Glutamate receptor, ionotropic kainate 2 / Glutamate receptor 6 / GluR-6 / GluR6


Mass: 29371.633 Da / Num. of mol.: 3 / Mutation: K494E, I749L, Q753K, E757Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Grik2, Glur6 / Plasmid: pET22 (modified) / Production host: Escherichia coli (E. coli) / Strain (production host): Origami B (DE3) / References: UniProt: P42260
#2: Chemical ChemComp-GLU / GLUTAMIC ACID


Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C5H9NO4
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 538 / 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: 2.75 Å3/Da / Density % sol: 55.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: Reservoir: 1.5 M Ammonium Sulfate, 0.1 M NaCl, 0.1 M HEPES. 0.015 M Na Acetate; Protein: 12-22 mg/ml, 10 mM L-glutamate, 20 mM NaCl, 1 mM EDTA, pH 7.0, pH 7.2, 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: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 19, 2005
RadiationMonochromator: Si 220 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.96→29.79 Å / Num. all: 68095 / Num. obs: 68095 / % possible obs: 99.92 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 6.5 % / Biso Wilson estimate: 30.4 Å2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 13
Reflection shellResolution: 1.96→2.03 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.452 / Mean I/σ(I) obs: 3.8 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
SERGUIdata collection
MAR345data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 17SY

17sy


Resolution: 1.96→30 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.948 / SU B: 5.727 / SU ML: 0.088 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: ANISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.139 / ESU R Free: 0.132 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21055 3668 5.1 %RANDOM
Rwork0.17208 ---
all0.17404 68095 --
obs0.17404 68095 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 30.993 Å2
Baniso -1Baniso -2Baniso -3
1--0.41 Å20 Å20 Å2
2---0.41 Å20 Å2
3---0.82 Å2
Refinement stepCycle: LAST / Resolution: 1.96→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6094 0 35 538 6667
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0226463
X-RAY DIFFRACTIONr_angle_refined_deg1.6711.9738746
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.5455812
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.7224.296284
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.182151210
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.3671539
X-RAY DIFFRACTIONr_chiral_restr0.1260.2961
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024837
X-RAY DIFFRACTIONr_nbd_refined0.2280.33205
X-RAY DIFFRACTIONr_nbtor_refined0.3230.54670
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2220.51008
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2130.359
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2820.536
X-RAY DIFFRACTIONr_mcbond_it1.60224065
X-RAY DIFFRACTIONr_mcangle_it2.36936401
X-RAY DIFFRACTIONr_scbond_it1.82422751
X-RAY DIFFRACTIONr_scangle_it2.7332345
LS refinement shellResolution: 1.96→2.011 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.233 258 -
Rwork0.189 4990 -
obs--99.98 %
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)
11.98710.17710.3511.43020.58422.05850.08940.12580.0346-0.0935-0.070.0510.06350.1717-0.0194-0.00980.0333-0.0080.0316-0.05250.025931.54410.53911.483
24.2126-1.2894-0.12640.9233-0.28880.98310.15770.00520.5672-0.0577-0.0413-0.2708-0.0445-0.0091-0.1164-0.01610.01630.0379-0.0005-0.06690.143616.91128.97116.886
32.29081.15680.37183.7150.85711.80170.0555-0.11730.1005-0.0056-0.0101-0.05510.05590.2823-0.0454-0.04450.0011-0.00020.0694-0.06770.007637.98115.06821.578
41.4681-0.0663-0.21240.1311-0.07861.2150.06890.0387-0.1476-0.0261-0.0149-0.01940.0289-0.0834-0.0540.0075-0.0196-0.04390.04550.00620.035836.81813.50246.509
52.6627-1.0311.92171.3101-1.05251.58660.1562-0.1247-0.2861-0.08960.02080.18760.1116-0.1183-0.177-0.0317-0.0147-0.03130.10610.00560.029615.29112.40842.637
62.8431-0.40451.41862.0347-0.45213.764-0.0612-0.23990.33560.08290.0328-0.0068-0.4017-0.3530.0284-0.01550.0185-0.0060.0515-0.01140.052831.9127.21653.383
73.22010.4993-0.54952.6503-0.41661.6226-0.0329-0.8506-0.16350.4391-0.01880.1798-0.0315-0.17510.0518-0.0183-0.01460.04350.390.0754-0.064723.89116.378.99
83.744-1.5526-1.08915.93152.52193.57680.0307-0.52830.4832-0.2218-0.10660.0858-0.4814-0.36780.0758-0.05790.1074-0.04290.1552-0.16580.037620.13638.16970.165
92.36660.2650.72942.22940.42583.0888-0.0588-0.5692-0.24280.04290.01940.25670.2144-0.64770.0394-0.1092-0.08660.03390.26030.07820.029719.36312.91367.39
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA4 - 1084 - 108
2X-RAY DIFFRACTION2AA109 - 214109 - 214
3X-RAY DIFFRACTION3AA215 - 257215 - 257
4X-RAY DIFFRACTION4BB1 - 1091 - 109
5X-RAY DIFFRACTION5BB110 - 227110 - 227
6X-RAY DIFFRACTION6BB228 - 257228 - 257
7X-RAY DIFFRACTION7CC3 - 1063 - 106
8X-RAY DIFFRACTION8CC107 - 215107 - 215
9X-RAY DIFFRACTION9CC216 - 257216 - 257

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