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- PDB-2xxv: Crystal structure of the GluK2 (GluR6) M770K LBD dimer in complex... -

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Basic information

Entry
Database: PDB / ID: 2xxv
TitleCrystal structure of the GluK2 (GluR6) M770K LBD dimer in complex with kainate
ComponentsGLUTAMATE RECEPTOR, IONOTROPIC KAINATE 2
KeywordsTRANSPORT 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 / regulation of short-term neuronal synaptic plasticity / negative regulation of synaptic transmission, glutamatergic / 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 / regulation of short-term neuronal synaptic plasticity / negative regulation of synaptic transmission, glutamatergic / inhibitory postsynaptic potential / glutamate receptor activity / ubiquitin conjugating enzyme binding / regulation of JNK cascade / receptor clustering / modulation of excitatory postsynaptic potential / kainate selective glutamate receptor activity / ionotropic glutamate receptor complex / extracellularly glutamate-gated ion channel activity / behavioral fear response / positive regulation of synaptic transmission / neuronal action potential / glutamate-gated receptor activity / glutamate-gated calcium ion channel activity / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / dendrite cytoplasm / presynaptic modulation of chemical synaptic transmission / SNARE binding / hippocampal mossy fiber to CA3 synapse / regulation of membrane potential / excitatory postsynaptic potential / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / synaptic transmission, glutamatergic / PDZ domain binding / regulation of long-term neuronal synaptic plasticity / modulation of chemical synaptic transmission / postsynaptic density membrane / terminal bouton / intracellular calcium ion homeostasis / positive regulation of neuron apoptotic process / presynaptic membrane / scaffold protein binding / neuron apoptotic process / chemical synaptic transmission / perikaryon / negative regulation of neuron apoptotic process / postsynaptic membrane / postsynaptic density / axon / neuronal cell body / synapse / dendrite / ubiquitin protein ligase binding / glutamatergic synapse / identical protein binding / membrane / plasma membrane
Similarity search - Function
Ionotropic glutamate receptor, metazoa / Ligated ion channel L-glutamate- and glycine-binding site / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / Ligated ion channel L-glutamate- and glycine-binding site / Ligand-gated ion channel / : / 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 / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / Ligated ion channel L-glutamate- and glycine-binding site / Ligand-gated ion channel / : / 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
3-(CARBOXYMETHYL)-4-ISOPROPENYLPROLINE / Glutamate receptor ionotropic, kainate 2
Similarity search - Component
Biological speciesRATTUS NORVEGICUS (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsNayeem, N. / Mayans, O. / Green, T.
CitationJournal: J.Neurosci. / Year: 2011
Title: Conformational Flexibility of the Ligand-Binding Domain Dimer in Kainate Receptor Gating and Desensitization
Authors: Nayeem, N. / Mayans, O. / Green, T.
History
DepositionNov 12, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 9, 2011Provider: repository / Type: Initial release
Revision 1.1Apr 4, 2012Group: Database references / Refinement description / Version format compliance
Revision 1.2Jan 30, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,7105
Polymers59,2482
Non-polymers4623
Water9,026501
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2210 Å2
ΔGint-17.5 kcal/mol
Surface area22520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.260, 104.873, 113.589
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein GLUTAMATE RECEPTOR, IONOTROPIC KAINATE 2 / GLUTAMATE RECEPTOR 6 / GLUR-6 / GLUR6


Mass: 29623.928 Da / Num. of mol.: 2 / Fragment: LIGAND BINDING DOMAIN, RESIDUES 429-544,667-806 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) RATTUS NORVEGICUS (Norway rat) / Plasmid: PET21A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P42260
#2: Chemical ChemComp-KAI / 3-(CARBOXYMETHYL)-4-ISOPROPENYLPROLINE / KAINATE


Mass: 213.230 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15NO4 / Comment: neurotransmitter, agonist*YM
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 501 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, MET 770 TO LYS ENGINEERED RESIDUE IN CHAIN B, MET 770 TO LYS

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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: 2.46 Å3/Da / Density % sol: 50 % / Description: NONE
Crystal growMethod: vapor diffusion, hanging drop
Details: VAPOR DIFFUSION, HANGING DROP 27% PEG 4000, 6% PROPAN-2-OL, 80MM SODIUM ACETATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.7→19.9 Å / Num. obs: 55807 / % possible obs: 88.1 % / Observed criterion σ(I): -3 / Redundancy: 7.4 % / Biso Wilson estimate: 19.2 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 15.6
Reflection shellResolution: 1.7→1.74 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.81 / Mean I/σ(I) obs: 2.1 / % possible all: 91.5

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2XXT

2xxt


Resolution: 1.7→19.939 Å / SU ML: 0.18 / σ(F): 1.99 / Phase error: 19.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2035 2791 5 %
Rwork0.165 --
obs0.1669 55807 88.12 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.513 Å2 / ksol: 0.371 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.3329 Å20 Å20 Å2
2---2.9779 Å20 Å2
3---2.645 Å2
Refinement stepCycle: LAST / Resolution: 1.7→19.939 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3977 0 31 501 4509
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074083
X-RAY DIFFRACTIONf_angle_d1.0855506
X-RAY DIFFRACTIONf_dihedral_angle_d16.2251518
X-RAY DIFFRACTIONf_chiral_restr0.077617
X-RAY DIFFRACTIONf_plane_restr0.004690
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.72930.29631440.2412726X-RAY DIFFRACTION92
1.7293-1.76070.27441420.23322713X-RAY DIFFRACTION91
1.7607-1.79460.2991430.20692719X-RAY DIFFRACTION91
1.7946-1.83120.23071420.19712686X-RAY DIFFRACTION91
1.8312-1.8710.21861420.18362703X-RAY DIFFRACTION91
1.871-1.91450.22961420.18182686X-RAY DIFFRACTION90
1.9145-1.96230.22261410.18072679X-RAY DIFFRACTION90
1.9623-2.01530.23211410.17022689X-RAY DIFFRACTION90
2.0153-2.07450.22611410.15952675X-RAY DIFFRACTION89
2.0745-2.14140.19021400.14642664X-RAY DIFFRACTION89
2.1414-2.21790.19841410.14392677X-RAY DIFFRACTION89
2.2179-2.30650.18891390.14882639X-RAY DIFFRACTION88
2.3065-2.41130.17841390.15442639X-RAY DIFFRACTION88
2.4113-2.53820.18241380.15392626X-RAY DIFFRACTION88
2.5382-2.69690.20861380.16162620X-RAY DIFFRACTION87
2.6969-2.90460.23031380.17362627X-RAY DIFFRACTION87
2.9046-3.19580.23571350.16892568X-RAY DIFFRACTION86
3.1958-3.65580.18451370.15712591X-RAY DIFFRACTION85
3.6558-4.59650.17021340.14132559X-RAY DIFFRACTION83
4.5965-19.94080.16851340.15832530X-RAY DIFFRACTION80
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)
11.03540.646-0.43621.05720.31520.7323-0.12120.1684-0.18370.0518-0.01470.08750.173-0.17550.11410.1128-0.0390.01610.13280.00080.1488-41.661524.82114.0071
20.69460.2282-0.83831.24990.02491.1758-0.0335-0.00690.1235-0.11730.06020.0487-0.0155-0.0226-0.0260.0969-0.0333-0.02540.09790.03590.0979-29.164538.42575.8943
32.03540.1041-0.52911.43010.15641.95750.05470.1943-0.1287-0.2159-0.0507-0.07980.0181-0.0905-0.00570.12360.00120.00810.14240.00730.099-18.299533.12511.7208
40.81930.77080.09130.72020.10210.67640.0599-0.05410.11530.0987-0.08940.1089-0.00180.00190.02110.1251-0.01390.02630.1281-0.00150.1304-35.262234.96222.3109
51.0301-1.29890.88081.7351-0.81921.627-0.20480.2115-0.05190.2049-0.0319-0.01230.06050.260.23490.13230.00660.0120.19560.01270.1205-28.120434.38875.84
60.73351.10540.13121.81720.46860.433-0.134-0.01590.1572-0.21330.1133-0.0668-0.1020.05270.02380.15710.0038-0.00570.1006-0.02580.1573-19.190163.114526.1463
71.00830.30120.47511.1316-0.50460.85430.0158-0.08440.06130.1559-0.01320.20830.0148-0.052-0.00150.1397-0.00320.0450.1128-0.01290.0945-26.196646.385135.2172
81.6966-0.29120.68152.0197-0.27582.11090.0219-0.23180.06280.27550.0223-0.11420.1079-0.1715-0.03010.13890.0087-0.01980.1262-0.00170.0806-16.889439.333540.6469
90.89270.63290.1231.34970.69440.7652-0.06250.09120.0872-0.2410.12740.0452-0.0575-0.0243-0.03210.1409-0.00890.00940.10960.01030.1281-24.313752.213518.526
100.915-0.4315-0.66430.37570.12331.1866-0.2316-0.266-0.03050.4306-0.2244-0.1028-0.4221-0.08640.33350.21560.0491-0.04710.20960.02270.1205-22.231347.140335.6421
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 429:483)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 484:677)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 678:762)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 763:805)
5X-RAY DIFFRACTION5(CHAIN A AND RESID 900)
6X-RAY DIFFRACTION6(CHAIN B AND RESID 429:483)
7X-RAY DIFFRACTION7(CHAIN B AND RESID 484:677)
8X-RAY DIFFRACTION8(CHAIN B AND RESID 678:762)
9X-RAY DIFFRACTION9(CHAIN B AND RESID 763:805)
10X-RAY DIFFRACTION10(CHAIN B AND RESID 900)

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