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- PDB-2xxy: Crystal structure of the GluK2 (GluR6) D776K LBD dimer in complex... -

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Basic information

Entry
Database: PDB / ID: 2xxy
TitleCrystal structure of the GluK2 (GluR6) D776K 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 / glutamate receptor activity / ubiquitin conjugating enzyme binding / negative regulation of synaptic transmission, glutamatergic / regulation of JNK cascade ...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 / glutamate receptor activity / ubiquitin conjugating enzyme binding / negative regulation of synaptic transmission, glutamatergic / regulation of JNK cascade / inhibitory postsynaptic potential / receptor clustering / kainate selective glutamate receptor activity / modulation of excitatory postsynaptic potential / extracellularly glutamate-gated ion channel activity / ionotropic glutamate receptor complex / positive regulation of synaptic transmission / behavioral fear response / 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 / presynaptic modulation of chemical synaptic transmission / dendrite cytoplasm / hippocampal mossy fiber to CA3 synapse / SNARE binding / 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 / postsynaptic density membrane / modulation of chemical synaptic transmission / intracellular calcium ion homeostasis / terminal bouton / positive regulation of neuron apoptotic process / presynaptic membrane / neuron apoptotic process / scaffold protein binding / perikaryon / chemical synaptic transmission / negative regulation of neuron apoptotic process / postsynaptic membrane / postsynaptic density / axon / neuronal cell body / ubiquitin protein ligase binding / synapse / dendrite / 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: 3 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 1.1Mar 28, 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
C: GLUTAMATE RECEPTOR, IONOTROPIC KAINATE 2
D: GLUTAMATE RECEPTOR, IONOTROPIC KAINATE 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,4138
Polymers118,5604
Non-polymers8534
Water00
1
A: GLUTAMATE RECEPTOR, IONOTROPIC KAINATE 2
B: GLUTAMATE RECEPTOR, IONOTROPIC KAINATE 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,7074
Polymers59,2802
Non-polymers4262
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2150 Å2
ΔGint-8.8 kcal/mol
Surface area21610 Å2
MethodPISA
2
C: GLUTAMATE RECEPTOR, IONOTROPIC KAINATE 2
D: GLUTAMATE RECEPTOR, IONOTROPIC KAINATE 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,7074
Polymers59,2802
Non-polymers4262
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2250 Å2
ΔGint-9.2 kcal/mol
Surface area21610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.665, 99.442, 124.627
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN C AND NOT ((RESSEQ 447:454) OR (RESSEQ 484) OR...
211CHAIN A AND NOT ((RESSEQ 447:454) OR (RESSEQ 484) OR...
311CHAIN B AND NOT ((RESSEQ 447:454) OR (RESSEQ 484) OR...
411CHAIN D AND NOT ((RESSEQ 447:454) OR (RESSEQ 484) OR...

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Components

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


Mass: 29640.037 Da / Num. of mol.: 4 / 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.: 4 / Source method: obtained synthetically / Formula: C10H15NO4
Compound detailsENGINEERED RESIDUE IN CHAIN A, ASP 776 TO LYS ENGINEERED RESIDUE IN CHAIN B, ASP 776 TO LYS ...ENGINEERED RESIDUE IN CHAIN A, ASP 776 TO LYS ENGINEERED RESIDUE IN CHAIN B, ASP 776 TO LYS ENGINEERED RESIDUE IN CHAIN C, ASP 776 TO LYS ENGINEERED RESIDUE IN CHAIN D, ASP 776 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: 2.27 Å3/Da / Density % sol: 46 % / Description: NONE
Crystal growMethod: vapor diffusion, hanging drop
Details: VAPOR DIFFUSION, HANGING DROP 21% PEG 4000, 3% PROPAN-2-OL, 80MM SODIUM ACETATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 1.0332
DetectorType: ADSC
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 3→19.8 Å / Num. obs: 21368 / % possible obs: 97.5 % / Observed criterion σ(I): -3 / Redundancy: 7.6 % / Biso Wilson estimate: 37.25 Å2 / Rmerge(I) obs: 0.18 / Net I/σ(I): 14.2
Reflection shellResolution: 3→3.08 Å / Redundancy: 8.2 % / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 3.5 / % possible all: 98.7

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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: 3→19.846 Å / SU ML: 0.36 / σ(F): 1.99 / Phase error: 28.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2642 1058 4.9 %
Rwork0.222 --
obs0.2242 21367 97.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 16.322 Å2 / ksol: 0.302 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--13.3219 Å20 Å20 Å2
2---6.5217 Å20 Å2
3---18.7664 Å2
Refinement stepCycle: LAST / Resolution: 3→19.846 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7920 0 60 0 7980
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0088131
X-RAY DIFFRACTIONf_angle_d1.14710959
X-RAY DIFFRACTIONf_dihedral_angle_d16.7193025
X-RAY DIFFRACTIONf_chiral_restr0.0761229
X-RAY DIFFRACTIONf_plane_restr0.0031368
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11C1786X-RAY DIFFRACTIONPOSITIONAL
12A1786X-RAY DIFFRACTIONPOSITIONAL0.052
13B1786X-RAY DIFFRACTIONPOSITIONAL0.045
14D1786X-RAY DIFFRACTIONPOSITIONAL0.052
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.13610.36721320.3342504X-RAY DIFFRACTION98
3.1361-3.30070.41021350.31032529X-RAY DIFFRACTION99
3.3007-3.50640.32411220.27152506X-RAY DIFFRACTION99
3.5064-3.77550.24181270.2412553X-RAY DIFFRACTION98
3.7755-4.15230.24081370.20362511X-RAY DIFFRACTION98
4.1523-4.74590.20761350.16462552X-RAY DIFFRACTION98
4.7459-5.95250.22741300.17532547X-RAY DIFFRACTION97
5.9525-19.84640.20451400.16782607X-RAY DIFFRACTION95
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)
10.1583-0.10030.07080.4255-0.10510.221-0.05890.1252-0.0212-0.03480.0770.2052-0.12360.0391-0.01350.0951-0.0116-0.04820.10560.06760.0459-24.78766.4381-19.0054
21.15320.20930.2270.75420.08110.3911-0.23210.3417-0.3935-0.16940.32260.01470.06990.122-0.07450.1465-0.06290.00310.1909-0.07530.0797-5.9255-2.0643-26.4235
30.9897-0.23150.19660.1177-0.04080.2135-0.018-0.2085-0.34050.03730.2075-0.0171-0.06240.1519-0.1030.07680.0046-0.04760.199-0.03180.1312-0.1385-3.57463.9487
41.6982-0.61630.53060.2338-0.16350.73430.0844-0.0752-0.6001-0.05890.11420.23870.07980.07980.07460.05310.0050.03790.00120.08420.0114-20.503-11.64165.5504
50.15590.0337-0.00190.3810.21690.3357-0.2257-0.0571-0.31380.12880.08260.4677-0.0508-0.0714-0.12610.14590.05350.23880.05490.13910.4041-65.03823.23336.4916
60.2726-0.1359-0.22670.25920.20111.1818-0.1863-0.1238-0.08630.04790.15610.2046-0.129-0.0196-0.40630.08880.05960.10480.11110.0580.0451-44.821811.79446.3814
70.16310.1192-0.02530.3333-0.08110.1318-0.0777-0.010.0291-0.07120.02720.08020.06670.03540.08240.10650.00960.08920.0188-0.00020.2497-42.0396-5.9436-18.3279
81.01440.2479-0.75010.0912-0.15660.53950.00010.5705-0.1270.02620.2975-0.05540.1495-0.57460.0834-0.2424-0.10530.04910.23940.07280.402-61.16623.513-23.8733
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 431:483 OR RESID 763:799)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 484:762)
3X-RAY DIFFRACTION3CHAIN B AND (RESID 431:483 OR RESID 763:799)
4X-RAY DIFFRACTION4(CHAIN B AND RESID 484:762)
5X-RAY DIFFRACTION5CHAIN C AND (RESID 431:483 OR RESID 763:799)
6X-RAY DIFFRACTION6(CHAIN C AND RESID 484:762)
7X-RAY DIFFRACTION7CHAIN D AND (RESID 431:483 OR RESID 763:799)
8X-RAY DIFFRACTION8(CHAIN D AND RESID 484:762)

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