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

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Basic information

Entry
Database: PDB / ID: 2xxw
TitleCrystal structure of the GluK2 (GluR6) D776K LBD dimer in complex with glutamate
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 / 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: 2.3 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 1.1Apr 4, 2012Group: Data collection / Database references ...Data collection / 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)59,6105
Polymers59,2802
Non-polymers3303
Water3,063170
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2380 Å2
ΔGint-19.3 kcal/mol
Surface area22720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.687, 106.821, 112.854
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: 29640.037 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) / Variant (production host): PLYSS / References: UniProt: P42260
#2: Chemical ChemComp-GLU / GLUTAMIC ACID


Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H9NO4
#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.: 170 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, ASP 776 TO LYS ENGINEERED RESIDUE IN CHAIN B, 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: 2.42 Å3/Da / Density % sol: 49 % / Description: NONE
Crystal growMethod: vapor diffusion, hanging drop
Details: VAPOR DIFFUSION, HANGING DROP 21% PEG 4000, 80MM SODIUM ACETATE
PH range: NULL; NULL

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineIDWavelength
SYNCHROTRONBESSY 14.210.91841
SYNCHROTRONDiamond I0221.5498
Detector
TypeIDDetector
RAYONIX1CCD
ADSC CCD2CCD
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2Mx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.918411
21.54981
ReflectionResolution: 2.3→30 Å / Num. obs: 25332 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Biso Wilson estimate: 40.14 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 13.2
Reflection shellResolution: 2.3→2.36 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 2 / % possible all: 98.3

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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 2XXR

2xxr


Resolution: 2.3→29.974 Å / SU ML: 0.34 / σ(F): 1.99 / Phase error: 24.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2439 1266 5 %
Rwork0.191 --
obs0.1936 25332 99.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.041 Å2 / ksol: 0.321 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-3.8526 Å20 Å20 Å2
2---8.1439 Å20 Å2
3---4.2912 Å2
Refinement stepCycle: LAST / Resolution: 2.3→29.974 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4018 0 21 170 4209
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044112
X-RAY DIFFRACTIONf_angle_d0.7625537
X-RAY DIFFRACTIONf_dihedral_angle_d16.4351531
X-RAY DIFFRACTIONf_chiral_restr0.056615
X-RAY DIFFRACTIONf_plane_restr0.003696
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.39210.31461380.25612626X-RAY DIFFRACTION98
2.3921-2.50090.31051390.24592631X-RAY DIFFRACTION100
2.5009-2.63270.30491400.23122665X-RAY DIFFRACTION100
2.6327-2.79750.31531380.22822653X-RAY DIFFRACTION100
2.7975-3.01330.2871410.22042676X-RAY DIFFRACTION100
3.0133-3.31620.29891400.20872650X-RAY DIFFRACTION100
3.3162-3.79520.23731410.18932687X-RAY DIFFRACTION99
3.7952-4.77850.2151420.15062697X-RAY DIFFRACTION99
4.7785-29.97690.17471470.1582781X-RAY DIFFRACTION98
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)
11.05730.80610.28271.38470.06030.8004-0.1357-0.02810.3491-0.18720.061-0.154-0.1144-0.01300.30290.0121-0.01370.215-0.04920.3148-20.86245.4888-33.0374
21.9274-0.29840.9411.879-0.48961.1730.031-0.34430.0190.1904-0.03520.03880.0702-0.20880.00010.2527-0.0148-0.01050.2695-0.03260.1776-20.6348-10.4359-18.0708
31.12492.0329-1.66043.6742-3.00082.4502-0.1687-0.9462-0.4101-0.09180.3960.3888-0.1165-0.3717-0.40.5964-0.00810.06490.4524-0.08130.345-22.3716-6.5889-20.9794
41.83430.88720.00640.8363-0.34761.3430.0143-0.147-0.16250.0441-0.0486-0.16470.1248-0.1125-0.00010.2333-0.0321-0.00360.24540.05040.2605-37.5926-24.7327-39.664
52.05040.56890.34281.948-0.43631.6752-0.02720.1989-0.2194-0.3625-0.0315-0.370.16320.1705-00.28010.02140.04520.26250.02680.2559-22.3072-17.2246-53.405
61.82571.85711.84941.88961.88061.87340.3492-0.02720.1048-0.19510.0179-0.0462-0.0186-0.0481-0.09320.3358-0.0342-0.02290.4802-0.07360.2889-26.7443-17.5762-50.8348
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 429:483 OR RESID 763:805)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 484:762)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 900)
4X-RAY DIFFRACTION4CHAIN B AND (RESID 429:483 OR RESID 763:805)
5X-RAY DIFFRACTION5(CHAIN B AND RESID 484:762)
6X-RAY DIFFRACTION6(CHAIN B AND RESID 900)

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