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- PDB-3g3j: Crystal structure of the GluR6 ligand binding domain dimer I442H ... -

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Basic information

Entry
Database: PDB / ID: 3g3j
TitleCrystal structure of the GluR6 ligand binding domain dimer I442H K494E K665R I749L Q753K mutant with glutamate and NaCl at 1.32 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 / FOURIER SYNTHESIS / Resolution: 1.321 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: Advisory / Source and taxonomy / Category: entity_src_gen / pdbx_unobs_or_zero_occ_atoms
Revision 1.3Nov 1, 2017Group: Refinement description / Category: software
Revision 1.4Oct 20, 2021Group: Advisory / Database references / Derived calculations
Category: database_2 / pdbx_unobs_or_zero_occ_atoms ...database_2 / pdbx_unobs_or_zero_occ_atoms / 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)59,30810
Polymers58,8512
Non-polymers4578
Water11,133618
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2940 Å2
ΔGint-70 kcal/mol
Surface area22840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.915, 113.710, 51.939
Angle α, β, γ (deg.)90.00, 115.31, 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: 29425.621 Da / Num. of mol.: 2 / Fragment: residues 429-544, 667-806 / Mutation: I473H, K525E, K696R, I780L, Q784K
Source method: isolated from a genetically manipulated source
Details: The I442H K494E K665R I749L and Q753K mutations were created intentionally. The 1st residue is a vector encoded affinity tag fragment. Residues 398-513 and 636 -775 are coupled by a ...Details: The I442H K494E K665R I749L and Q753K mutations were created intentionally. The 1st residue is a vector encoded affinity tag fragment. Residues 398-513 and 636 -775 are coupled by a synthetic GT peptide. The numbering is for the mature prot ein after cleavage of the 31 AA 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.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 618 / 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: 2.31 Å3/Da / Density % sol: 46.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 15% PEG 4K, 15% 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: Dec 15, 2007
RadiationMonochromator: Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.32→35 Å / Num. obs: 124517 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 14.11 Å2 / Rmerge(I) obs: 0.044 / Net I/σ(I): 19.7
Reflection shellResolution: 1.32→1.37 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.369 / Mean I/σ(I) obs: 3.4 / % possible all: 99.2

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.321→34.516 Å / SU ML: 0.17 / 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
Rfree0.1789 6231 5.01 %RANDOM
Rwork0.1561 ---
all0.1573 124266 --
obs0.1573 124266 99.74 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 52.808 Å2 / ksol: 0.414 e/Å3
Refinement stepCycle: LAST / Resolution: 1.321→34.516 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8753 0 39 618 9410
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.018905
X-RAY DIFFRACTIONf_angle_d1.11416188
X-RAY DIFFRACTIONf_chiral_restr0.089677
X-RAY DIFFRACTIONf_plane_restr0.0061368
X-RAY DIFFRACTIONf_dihedral_angle_d14.8652307
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.321-1.3360.22912140.22193767X-RAY DIFFRACTION95
1.336-1.35180.2332330.21123858X-RAY DIFFRACTION99
1.3518-1.36820.22512060.20953962X-RAY DIFFRACTION100
1.3682-1.38560.24432040.19943903X-RAY DIFFRACTION100
1.3856-1.40380.18551960.19173980X-RAY DIFFRACTION100
1.4038-1.4230.20932060.18243894X-RAY DIFFRACTION100
1.423-1.44340.19642040.17473941X-RAY DIFFRACTION100
1.4434-1.46490.20951810.16683947X-RAY DIFFRACTION100
1.4649-1.48780.17362270.15883935X-RAY DIFFRACTION100
1.4878-1.51220.17741960.1523898X-RAY DIFFRACTION100
1.5122-1.53830.17332030.15064006X-RAY DIFFRACTION100
1.5383-1.56620.17881880.14623897X-RAY DIFFRACTION100
1.5662-1.59640.16622030.14613955X-RAY DIFFRACTION100
1.5964-1.62890.16642020.1413937X-RAY DIFFRACTION100
1.6289-1.66440.18362020.14033937X-RAY DIFFRACTION100
1.6644-1.70310.16621950.14773955X-RAY DIFFRACTION100
1.7031-1.74570.17542040.14553946X-RAY DIFFRACTION100
1.7457-1.79290.17792100.14643929X-RAY DIFFRACTION100
1.7929-1.84560.17332130.14393939X-RAY DIFFRACTION100
1.8456-1.90520.162120.14453926X-RAY DIFFRACTION100
1.9052-1.97330.17122080.14423967X-RAY DIFFRACTION100
1.9733-2.05230.15442160.13153920X-RAY DIFFRACTION100
2.0523-2.14570.16022050.12793945X-RAY DIFFRACTION100
2.1457-2.25880.14572070.12863951X-RAY DIFFRACTION100
2.2588-2.40020.15952200.13633935X-RAY DIFFRACTION100
2.4002-2.58550.17282140.14363940X-RAY DIFFRACTION100
2.5855-2.84560.1842270.14973949X-RAY DIFFRACTION100
2.8456-3.25710.17132130.14713961X-RAY DIFFRACTION100
3.2571-4.10250.15092250.13893942X-RAY DIFFRACTION100
4.1025-34.52830.17921970.15744013X-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)
10.75290.4013-0.0040.97-0.22050.8205-0.06250.09610.1111-0.24860.05650.0059-0.07420.0152-0.00440.1556-0.00540.01360.09710.02840.098414.74429.7692-5.5416
20.61120.27950.35470.96290.27230.53640.0131-0.00520.07590.0535-0.0095-0.055-0.00630.0265-0.04070.0619-0.00330.01290.048100.061220.62831.266714.6013
30.10790.0379-0.07540.6765-0.10370.3672-0.01160.1655-0.0439-0.12370.0331-0.13530.07690.0761-0.02840.13230.0080.02540.1227-0.00170.120519.662214.1161-1.5707
40.9294-0.0826-0.02590.74750.07410.73710.0208-0.066-0.05790.01390.00670.07340.0226-0.046-0.02750.066-0.0073-0.00870.08360.01010.07844.97630.879316.695
51.1698-0.3154-0.06640.5402-0.01520.80430.0398-0.0564-0.07940.007-0.0265-0.07750.06370.07830.00680.01110.006-0.00480.0296-0.0010.030727.4244-4.843311.2925
60.2798-0.0065-0.11620.5236-0.24520.27040.0288-0.05720.07980.04460.0270.0165-0.0880.016-0.04970.0944-0.00250.00420.0929-0.01270.09038.050813.189917.318
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and (resid 3:86)
2X-RAY DIFFRACTION2chain A and (resid 87:226)
3X-RAY DIFFRACTION3chain A and (resid 227:253)
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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