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- PDB-3g3g: Crystal structure of the GluR6 ligand binding domain dimer K665R ... -

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Basic information

Entry
Database: PDB / ID: 3g3g
TitleCrystal structure of the GluR6 ligand binding domain dimer K665R mutant with glutamate and NaCl at 1.3 Angstrom resolution
ComponentsGlutamate receptor, ionotropic kainate 2
KeywordsMEMBRANE PROTEIN / Cell junction / Cell membrane / Glycoprotein / Ion transport / Ionic channel / Membrane / Postsynaptic cell membrane / Receptor / RNA editing / Synapse / Transmembrane / Transport
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: 1.303 Å
AuthorsChaudhry, C. / Mayer, M.L.
CitationJournal: Embo J. / Year: 2009
Title: Stability of ligand-binding domain dimer assembly controls kainate receptor desensitization.
Authors: Chaudhry, C. / Weston, M.C. / Schuck, P. / Rosenmund, C. / Mayer, M.L.
History
DepositionFeb 2, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 2, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 26, 2017Group: Source and taxonomy / Category: entity_src_gen
Revision 1.3Nov 1, 2017Group: Refinement description / Category: software
Revision 1.4Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / 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_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _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

Downloads & links

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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)59,2469
Polymers58,7992
Non-polymers4477
Water11,854658
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2850 Å2
ΔGint-60 kcal/mol
Surface area22550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.990, 113.532, 52.022
Angle α, β, γ (deg.)90.00, 115.24, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe native protein is believed to be a dimer of dimers; only 1 copy of the dimer formed by chains A and B is present in this crystal form.

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Components

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


Mass: 29399.648 Da / Num. of mol.: 2 / Fragment: residues 429-544, 667-806 / Mutation: K696R
Source method: isolated from a genetically manipulated source
Details: The K665R mutation was created intentionally. The 1st residue is a vector encod ed affinity tag fragment. Residues 398-513 and 636-775 are coupled by a syntheti c GT peptide. The numbering ...Details: The K665R mutation was created intentionally. The 1st residue is a vector encod ed affinity tag fragment. Residues 398-513 and 636-775 are coupled by a syntheti c GT peptide. The numbering is for the mature protein after cleavage of the 31 A A signal peptide.
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: GriK2 / Plasmid: pET22B modified / Production host: Escherichia coli (E. coli) / Strain (production host): OrigamiB (DE3) / 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.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 658 / 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: 2.32 Å3/Da / Density % sol: 46.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 15% PEG 4K, 13% ISOPROPANOL, 0.1 M NaCitrate, pH 5.6, 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: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 8, 2008
RadiationMonochromator: Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.3→30 Å / Num. obs: 130744 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Biso Wilson estimate: 11.87 Å2 / Rmerge(I) obs: 0.039 / Net I/σ(I): 15.9
Reflection shellResolution: 1.3→1.35 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.309 / Mean I/σ(I) obs: 3.38 / % possible all: 91.4

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.303→29.256 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ML
Details: Refinement was started with Refmac_5.2. The final rounds of refinement were performed with phenix and included occupancy refinement for ions, and for residues with alternative conformations.
RfactorNum. reflection% reflectionSelection details
Rfree0.1676 6491 5.01 %RANDOM
Rwork0.1463 ---
all0.1474 129531 --
obs0.1474 129531 99.64 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 55.247 Å2 / ksol: 0.425 e/Å3
Refinement stepCycle: LAST / Resolution: 1.303→29.256 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8702 0 38 663 9403
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0168863
X-RAY DIFFRACTIONf_angle_d1.39216115
X-RAY DIFFRACTIONf_chiral_restr0.121665
X-RAY DIFFRACTIONf_plane_restr0.0081343
X-RAY DIFFRACTIONf_dihedral_angle_d14.2222296
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3031-1.31790.24151930.21753724X-RAY DIFFRACTION91
1.3179-1.33340.23282230.20554052X-RAY DIFFRACTION99
1.3334-1.34970.20892560.18744073X-RAY DIFFRACTION100
1.3497-1.36680.20112170.17864126X-RAY DIFFRACTION100
1.3668-1.38480.19142100.17214108X-RAY DIFFRACTION100
1.3848-1.40370.19772090.16424110X-RAY DIFFRACTION100
1.4037-1.42380.16852080.1574091X-RAY DIFFRACTION100
1.4238-1.4450.17652180.15154120X-RAY DIFFRACTION100
1.445-1.46760.17091880.14714120X-RAY DIFFRACTION100
1.4676-1.49170.16952280.13844110X-RAY DIFFRACTION100
1.4917-1.51740.152090.13044085X-RAY DIFFRACTION100
1.5174-1.5450.15852080.12654152X-RAY DIFFRACTION100
1.545-1.57470.16132010.12674141X-RAY DIFFRACTION100
1.5747-1.60680.14282090.12584090X-RAY DIFFRACTION100
1.6068-1.64180.15482110.12454127X-RAY DIFFRACTION100
1.6418-1.680.16072200.13034135X-RAY DIFFRACTION100
1.68-1.7220.16511890.13514111X-RAY DIFFRACTION100
1.722-1.76850.16842280.12734073X-RAY DIFFRACTION100
1.7685-1.82050.14922260.13144151X-RAY DIFFRACTION100
1.8205-1.87930.1432130.13424087X-RAY DIFFRACTION100
1.8793-1.94650.15072400.13184107X-RAY DIFFRACTION100
1.9465-2.02440.16682080.13044121X-RAY DIFFRACTION100
2.0244-2.11650.16242180.12614138X-RAY DIFFRACTION100
2.1165-2.2280.142090.1244112X-RAY DIFFRACTION100
2.228-2.36760.14282310.12654110X-RAY DIFFRACTION100
2.3676-2.55030.16132290.14054125X-RAY DIFFRACTION100
2.5503-2.80670.18852360.14394098X-RAY DIFFRACTION100
2.8067-3.21240.17252110.14884146X-RAY DIFFRACTION100
3.2124-4.04560.13722400.13734113X-RAY DIFFRACTION100
4.0456-29.26360.1812050.15164184X-RAY DIFFRACTION99
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)
10.74560.3053-0.09291.3219-0.12250.9459-0.05380.10080.1087-0.25670.06650.0263-0.0867-0.0025-0.02120.1316-0.01050.00150.08520.02280.08514.814829.4656-5.4539
20.62910.37980.30691.42160.44920.61820.0225-0.01450.04650.08520.0078-0.09230.00040.0454-0.02340.0598-0.00240.00690.0522-0.00260.054921.661731.836815.3981
30.46860.07920.04540.8755-0.11840.4595-0.01730.0709-0.0255-0.1410.0126-0.07240.09950.0333-0.00510.1021-0.00150.01080.08220.00450.074717.215815.3701-1.5769
41.0146-0.0496-0.210.8260.0530.7140.0149-0.0558-0.0560.02770.01330.06890.0183-0.0329-0.02550.0265-0.0044-0.00910.04090.01060.03745.09890.647916.6813
51.3402-0.19470.08920.7258-0.02020.73430.0343-0.0343-0.0689-0.0032-0.0337-0.05420.0560.0698-0.00110.0480.00520.00050.06310.00180.057427.4059-4.906211.581
60.5174-0.0246-0.08910.5479-0.25630.52760.0302-0.04650.11050.0710.01010.0268-0.09030.0232-0.040.0782-0.00220.00430.0715-0.00750.07777.956212.980117.5559
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and (resid 3:86)
2X-RAY DIFFRACTION2chain A and (resid 87:218)
3X-RAY DIFFRACTION3chain A and (resid 219:253)
4X-RAY DIFFRACTION4chain B and (resid 2:108)
5X-RAY DIFFRACTION5chain B and (resid 109:216)
6X-RAY DIFFRACTION6chain B and (resid 217:253)

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