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- PDB-3g3i: Crystal structure of the GluR6 ligand binding domain dimer I442H ... -

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Basic information

Entry
Database: PDB / ID: 3g3i
TitleCrystal structure of the GluR6 ligand binding domain dimer I442H K494E I749L Q753K mutant with glutamate and NaCl at 1.37 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 / extracellularly glutamate-gated ion channel activity / regulation of JNK cascade / kainate selective glutamate receptor activity / ionotropic glutamate receptor complex / behavioral fear response / neuronal action potential / positive regulation of synaptic transmission / 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 / regulation of membrane potential / SNARE binding / excitatory postsynaptic potential / synaptic transmission, glutamatergic / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / PDZ domain binding / 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 / perikaryon / postsynaptic membrane / neuron apoptotic process / negative regulation of neuron apoptotic process / postsynaptic density / axon / neuronal cell body / glutamatergic synapse / dendrite / ubiquitin protein ligase binding / 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
GLUTAMIC ACID / Glutamate receptor ionotropic, kainate 2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.371 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 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _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)59,1948
Polymers58,7952
Non-polymers3996
Water12,466692
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2740 Å2
ΔGint-54 kcal/mol
Surface area22840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.087, 114.300, 52.319
Angle α, β, γ (deg.)90.00, 114.99, 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: 29397.609 Da / Num. of mol.: 2 / Fragment: residues 429-544, 667-806 / Mutation: I473H, K525E, I780L, Q784K
Source method: isolated from a genetically manipulated source
Details: The I442H K494E I749L and Q753K mutations were created intentionally. The 1st r esidue is a vector encoded affinity tag fragment. Residues 398-513 and 636-775 a re coupled by a synthetic GT ...Details: The I442H K494E I749L and Q753K mutations were created intentionally. The 1st r esidue is a vector encoded affinity tag fragment. Residues 398-513 and 636-775 a re coupled by a synthetic GT peptide. The numbering is for the mature protein af ter 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.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 692 / 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: 2.35 Å3/Da / Density % sol: 47.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 18% 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: Feb 16, 2008
RadiationMonochromator: Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.37→30 Å / Num. obs: 113524 / % possible obs: 94.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.7 % / Biso Wilson estimate: 13.93 Å2 / Rmerge(I) obs: 0.038 / Net I/σ(I): 16.4
Reflection shellResolution: 1.37→1.42 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.241 / Mean I/σ(I) obs: 2.9 / % possible all: 89.3

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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: 1.371→28.687 Å / SU ML: 0.16 / Isotropic thermal model: ISOTROPIC AND TLS / 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
Rfree0.176 5438 4.99 %RANDOM
Rwork0.1493 ---
all0.1506 109022 --
obs0.1506 109022 95.93 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.238 Å2 / ksol: 0.413 e/Å3
Refinement stepCycle: LAST / Resolution: 1.371→28.687 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8858 0 37 694 9589
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.019029
X-RAY DIFFRACTIONf_angle_d1.13816439
X-RAY DIFFRACTIONf_chiral_restr0.096676
X-RAY DIFFRACTIONf_plane_restr0.0061373
X-RAY DIFFRACTIONf_dihedral_angle_d14.982347
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3706-1.38620.23151450.20613032X-RAY DIFFRACTION83
1.3862-1.40250.19581760.1853314X-RAY DIFFRACTION94
1.4025-1.41960.20581860.18013487X-RAY DIFFRACTION95
1.4196-1.43760.19241780.17023374X-RAY DIFFRACTION95
1.4376-1.45650.21781740.17273469X-RAY DIFFRACTION96
1.4565-1.47640.20861600.16183437X-RAY DIFFRACTION96
1.4764-1.49750.18572010.15823456X-RAY DIFFRACTION96
1.4975-1.51990.21491790.14673391X-RAY DIFFRACTION96
1.5199-1.54360.17851800.1393498X-RAY DIFFRACTION96
1.5436-1.56890.16651680.13763425X-RAY DIFFRACTION96
1.5689-1.5960.16671790.13823514X-RAY DIFFRACTION97
1.596-1.6250.16981720.13133462X-RAY DIFFRACTION97
1.625-1.65620.16081720.13313484X-RAY DIFFRACTION97
1.6562-1.690.15851960.13713496X-RAY DIFFRACTION97
1.69-1.72680.18031590.13593474X-RAY DIFFRACTION97
1.7268-1.7670.17091900.13733515X-RAY DIFFRACTION97
1.767-1.81110.17181840.13973490X-RAY DIFFRACTION97
1.8111-1.86010.1631990.14273510X-RAY DIFFRACTION98
1.8601-1.91480.17471920.14163495X-RAY DIFFRACTION98
1.9148-1.97660.15491900.13753510X-RAY DIFFRACTION98
1.9766-2.04720.15251800.12893534X-RAY DIFFRACTION98
2.0472-2.12920.1531880.12843533X-RAY DIFFRACTION98
2.1292-2.2260.15351840.13013522X-RAY DIFFRACTION98
2.226-2.34340.17361800.13523499X-RAY DIFFRACTION98
2.3434-2.49010.17382110.14213505X-RAY DIFFRACTION97
2.4901-2.68220.1691840.14953479X-RAY DIFFRACTION97
2.6822-2.95190.20371870.15513479X-RAY DIFFRACTION96
2.9519-3.37850.16811950.14393457X-RAY DIFFRACTION96
3.3785-4.25430.15871880.13463428X-RAY DIFFRACTION94
4.2543-28.69280.16691610.14783315X-RAY DIFFRACTION90
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)
10.92290.2205-0.08721.6367-0.19530.8255-0.02080.12360.1588-0.16950.09990.11-0.0668-0.0356-0.06990.09090.00120.00570.04960.04110.074414.112728.2022-2.8847
21.2081-0.05560.14712.30530.5120.98050.0039-0.06420.10610.0955-0.0085-0.1719-0.01330.06650.00910.1124-0.00170.00290.0897-0.00240.108324.40934.192917.8033
30.4230.135-0.2351.5094-0.43610.7101-0.00660.0047-0.0433-0.14170.0271-0.11960.08340.057-0.0030.11040.00180.0170.09490.00870.08819.343616.9265-0.0911
41.35490.0486-0.19011.03640.18750.79460.0052-0.09-0.05650.03180.02870.07920.0183-0.0609-0.03720.0405-0.006-0.0130.06370.01210.04725.17730.570616.5126
51.5065-0.11130.05811.086-0.07650.95430.0395-0.0418-0.0989-0.0108-0.0286-0.07510.05130.0753-0.00780.05260.0059-0.00770.07090.00020.062427.5251-4.860211.1531
60.7101-0.018-0.35170.9609-0.25191.18840.0856-0.08320.15480.06660.03250.0326-0.15460.0505-0.0840.0862-0.00520.0150.0808-0.01660.09128.656712.901717.9254
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and (resid 3:108)
2X-RAY DIFFRACTION2chain A and (resid 109:214)
3X-RAY DIFFRACTION3chain A and (resid 215:258)
4X-RAY DIFFRACTION4chain B and (resid 2:108)
5X-RAY DIFFRACTION5chain B and (resid 109:216)
6X-RAY DIFFRACTION6chain B and (resid 217:254)

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