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- PDB-3g3k: Crystal structure of the GluR6 ligand binding domain dimer I442H ... -

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Basic information

Entry
Database: PDB / ID: 3g3k
TitleCrystal structure of the GluR6 ligand binding domain dimer I442H K494E K665R I749L Q753K E757Q mutant with glutamate and NaCl at 1.24 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 / ISOPROPYL ALCOHOL / Glutamate receptor ionotropic, kainate 2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.24 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.pdbx_ptnr1_label_alt_id / _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)59,48713
Polymers58,8492
Non-polymers63811
Water13,097727
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4030 Å2
ΔGint-78 kcal/mol
Surface area22620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.133, 113.844, 52.098
Angle α, β, γ (deg.)90.00, 115.22, 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

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Protein , 1 types, 2 molecules AB

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


Mass: 29424.637 Da / Num. of mol.: 2 / Fragment: residues 429-544, 667-806 / Mutation: I473H, K525E, K696R, I780L, Q784K, E788Q
Source method: isolated from a genetically manipulated source
Details: The I442H K494E K665R I749L Q753K and E757Q mutations were created intentionall y. The 1st residue is a vector encoded affinity tag fragment. Residues 398-513 a nd 636-775 are coupled by a ...Details: The I442H K494E K665R I749L Q753K and E757Q mutations were created intentionall y. The 1st residue is a vector encoded affinity tag fragment. Residues 398-513 a nd 636-775 are coupled by a synthetic GT peptide. The numbering is for the matur e protein 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

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Non-polymers , 5 types, 738 molecules

#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.: 5 / 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: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 727 / 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: 2.33 Å3/Da / Density % sol: 47.23 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 17% PEG 4K, 12% ISOPROPANOL, 0.1M 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: Jul 27, 2008
RadiationMonochromator: Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.24→40 Å / Num. obs: 151197 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.6 % / Biso Wilson estimate: 11.5 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 18.5
Reflection shellResolution: 1.24→1.28 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.282 / Mean I/σ(I) obs: 3.39 / % possible all: 86.5

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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: 1.24→35.898 Å / SU ML: 0.14 / 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
Rfree0.165 7489 5.03 %RANDOM
Rwork0.1459 ---
all0.1469 149020 --
obs0.1469 149020 98.18 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.237 Å2 / ksol: 0.393 e/Å3
Refinement stepCycle: LAST / Resolution: 1.24→35.898 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9668 0 41 752 10461
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0179916
X-RAY DIFFRACTIONf_angle_d1.38818183
X-RAY DIFFRACTIONf_chiral_restr0.126734
X-RAY DIFFRACTIONf_plane_restr0.0081518
X-RAY DIFFRACTIONf_dihedral_angle_d14.972651
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2403-1.25440.23871720.22363189X-RAY DIFFRACTION67
1.2544-1.26910.22692060.21644077X-RAY DIFFRACTION85
1.2691-1.28460.22282430.19694547X-RAY DIFFRACTION95
1.2846-1.30090.19472830.18344752X-RAY DIFFRACTION100
1.3009-1.3180.19362360.17234824X-RAY DIFFRACTION100
1.318-1.3360.1932660.17394765X-RAY DIFFRACTION100
1.336-1.35510.1872940.16244761X-RAY DIFFRACTION100
1.3551-1.37540.17562350.15874828X-RAY DIFFRACTION100
1.3754-1.39690.17582530.15374747X-RAY DIFFRACTION100
1.3969-1.41980.16212600.14544832X-RAY DIFFRACTION100
1.4198-1.44420.14662350.14854780X-RAY DIFFRACTION100
1.4442-1.47050.17042300.14334850X-RAY DIFFRACTION100
1.4705-1.49880.18252610.13954822X-RAY DIFFRACTION100
1.4988-1.52940.15212460.13214781X-RAY DIFFRACTION100
1.5294-1.56260.16592330.13274795X-RAY DIFFRACTION100
1.5626-1.5990.14992570.13384827X-RAY DIFFRACTION100
1.599-1.6390.15472370.13214827X-RAY DIFFRACTION100
1.639-1.68330.16792560.13834791X-RAY DIFFRACTION100
1.6833-1.73280.15922250.13834842X-RAY DIFFRACTION100
1.7328-1.78870.16642630.13744783X-RAY DIFFRACTION100
1.7887-1.85270.15982600.144790X-RAY DIFFRACTION100
1.8527-1.92680.16982690.13874774X-RAY DIFFRACTION100
1.9268-2.01450.14632450.13464816X-RAY DIFFRACTION100
2.0145-2.12070.15172580.1264807X-RAY DIFFRACTION100
2.1207-2.25360.14042480.12354781X-RAY DIFFRACTION100
2.2536-2.42750.14352740.134805X-RAY DIFFRACTION100
2.4275-2.67180.16272610.1384784X-RAY DIFFRACTION100
2.6718-3.05820.17752610.14954847X-RAY DIFFRACTION100
3.0582-3.85230.14862780.13454800X-RAY DIFFRACTION100
3.8523-35.91330.15432440.14464907X-RAY DIFFRACTION100
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)
10.4660.2035-0.01870.6649-0.04790.4091-0.02770.05550.0728-0.1340.04310.0227-0.0377-0.0062-0.00880.11340.00030.00870.07720.02240.081914.180528.4575-3.1756
20.40310.0870.19650.49950.19960.51050.0155-0.00130.07950.0391-0.0223-0.0809-0.00790.0362-0.00230.092-0.00610.01090.0757-0.01110.104624.139133.819717.0593
30.0460.01510.040.3557-0.02580.21630.0050.01580.0181-0.11130.0198-0.07350.03910.02280.0020.10080.00390.01530.08520.00190.088219.351315.6481-0.7787
40.7035-0.0363-0.04380.46910.0870.43360.0066-0.0378-0.05950.01740.01540.05760.0194-0.0340.01620.0509-0.0038-0.00880.06430.00940.05955.14760.267116.6071
50.6618-0.159-0.08350.2366-0.08780.49760.0229-0.0236-0.0761-0.011-0.0218-0.04290.03330.034100.04080.0075-0.00670.054-0.00420.056127.4758-4.906411.7231
60.2416-0.0654-0.14760.3038-0.09430.20020.0392-0.03610.06770.06080.02030.0014-0.03210.01670.02250.0814-0.0019-0.00170.0769-0.0090.0739.633513.07519.1552
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and (resid 3:107)
2X-RAY DIFFRACTION2chain A and (resid 108:216)
3X-RAY DIFFRACTION3chain A and (resid 217:258)
4X-RAY DIFFRACTION4chain B and (resid 2:108)
5X-RAY DIFFRACTION5chain B and (resid 109:216)
6X-RAY DIFFRACTION6chain B and (resid 217:257)

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