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- PDB-3qxm: Crystal Structure of Human GluK2 Ligand-Binding Core in Complex w... -

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Basic information

Entry
Database: PDB / ID: 3qxm
TitleCrystal Structure of Human GluK2 Ligand-Binding Core in Complex with Novel Marine-Derived Toxins, Neodysiherbaine A
ComponentsGlutamate receptor ionotropic, kainate 2
KeywordsMEMBRANE PROTEIN / two domains / ligand-binding
Function / homology
Function and homology information


Activation of Na-permeable kainate receptors / mossy fiber rosette / detection of cold stimulus involved in thermoception / kainate selective glutamate receptor complex / regulation of short-term neuronal synaptic plasticity / negative regulation of synaptic transmission, glutamatergic / ubiquitin conjugating enzyme binding / regulation of JNK cascade / Activation of Ca-permeable Kainate Receptor / glutamate receptor signaling pathway ...Activation of Na-permeable kainate receptors / mossy fiber rosette / detection of cold stimulus involved in thermoception / kainate selective glutamate receptor complex / regulation of short-term neuronal synaptic plasticity / negative regulation of synaptic transmission, glutamatergic / ubiquitin conjugating enzyme binding / regulation of JNK cascade / Activation of Ca-permeable Kainate Receptor / glutamate receptor signaling pathway / inhibitory postsynaptic potential / receptor clustering / kainate selective glutamate receptor activity / modulation of excitatory postsynaptic potential / extracellularly glutamate-gated ion channel activity / positive regulation of synaptic transmission / behavioral fear response / neuronal action potential / 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 / SNARE binding / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / synaptic transmission, glutamatergic / PDZ domain binding / regulation of long-term neuronal synaptic plasticity / postsynaptic density membrane / modulation of chemical synaptic transmission / intracellular calcium ion homeostasis / terminal bouton / positive regulation of neuron apoptotic process / presynaptic membrane / neuron apoptotic process / scaffold protein binding / perikaryon / chemical synaptic transmission / negative regulation of neuron apoptotic process / ubiquitin protein ligase binding / glutamatergic synapse / identical protein binding / 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
Chem-NDZ / Glutamate receptor ionotropic, kainate 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsUnno, M. / Sasaki, M. / Ikeda-Saito, M.
CitationJournal: J.Mol.Biol. / Year: 2011
Title: Binding and Selectivity of the Marine Toxin Neodysiherbaine A and Its Synthetic Analogues to GluK1 and GluK2 Kainate Receptors.
Authors: Unno, M. / Shinohara, M. / Takayama, K. / Tanaka, H. / Teruya, K. / Doh-Ura, K. / Sakai, R. / Sasaki, M. / Ikeda-Saito, M.
History
DepositionMar 2, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 26, 2011Provider: repository / Type: Initial release
Revision 1.1Jun 28, 2017Group: Advisory / Database references ...Advisory / Database references / Source and taxonomy / Structure summary
Category: entity / entity_name_com ...entity / entity_name_com / entity_src_gen / pdbx_distant_solvent_atoms / struct_ref_seq_dif
Item: _entity.pdbx_description / _entity.pdbx_fragment ..._entity.pdbx_description / _entity.pdbx_fragment / _entity_name_com.name / _struct_ref_seq_dif.details
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)59,1564
Polymers58,5732
Non-polymers5832
Water8,539474
1
A: Glutamate receptor ionotropic, kainate 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5782
Polymers29,2871
Non-polymers2911
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Glutamate receptor ionotropic, kainate 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5782
Polymers29,2871
Non-polymers2911
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.353, 105.684, 57.999
Angle α, β, γ (deg.)90.00, 102.27, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Glutamate receptor ionotropic, kainate 2 / GluK2 / Excitatory amino acid receptor 4 / EAA4 / Glutamate receptor 6 / GluR6


Mass: 29286.527 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 429-544,UNP RESIDUES 667-806
Source method: isolated from a genetically manipulated source
Details: The fusion protein of RESIDUES 429-544 of GluR-6, the linker GLY-THR and 667-806 of GluR-6
Source: (gene. exp.) Homo sapiens (human) / Gene: GRIK2, GLUR6 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q13002
#2: Chemical ChemComp-NDZ / (2R,3aR,6R,7R,7aR)-2-[(2S)-2-amino-2-carboxyethyl]-6,7-dihydroxyhexahydro-2H-furo[3,2-b]pyran-2-carboxylic acid


Mass: 291.255 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H17NO8
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 474 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.37 Å3/Da / Density % sol: 48.1 %
Crystal growTemperature: 303 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 18-22% PEG4000, 2mM Tris, 1mM EDTA, 10mM NaCl, 10mM Sodium L-ascorbate monohydrate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 303K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 9, 2009
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.65→50 Å / Num. all: 67908 / Num. obs: 62566 / % possible obs: 96.11 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.65→1.68 Å / % possible all: 75.3

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
CNSrefinement
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3G3F

3g3f


Resolution: 1.65→29.92 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.95 / SU B: 4.619 / SU ML: 0.073 / Cross valid method: THROUGHOUT / ESU R Free: 0.105 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22118 3142 5 %RANDOM
Rwork0.18117 ---
all0.18321 62566 --
obs0.18321 59382 95.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.369 Å2
Baniso -1Baniso -2Baniso -3
1-2.81 Å20 Å2-0.19 Å2
2---1.07 Å20 Å2
3----1.82 Å2
Refinement stepCycle: LAST / Resolution: 1.65→29.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4003 0 40 474 4517
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0224216
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4971.9815720
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5865532
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.12524.208183
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.17715777
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.2811525
X-RAY DIFFRACTIONr_chiral_restr0.1220.2646
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0213117
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.6391.52555
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.63324137
X-RAY DIFFRACTIONr_scbond_it4.05331661
X-RAY DIFFRACTIONr_scangle_it6.3434.51569
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.65→1.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.395 163 -
Rwork0.329 3205 -
obs--70.27 %
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)
10.2178-0.0028-0.20810.91170.12251.13750.0186-0.0443-0.0648-0.05220.03570.01430.05340.0355-0.05420.01670.0031-0.01960.0280.00910.03660.052-18.75822.415
2147.7072-1.129117.46924.08320.03892.145-2.6657-1.87831.84940.89292.2280.4945-0.1985-0.00640.43770.4470.16450.17171.14360.28740.2018-6.80913.90930.859
30.069-0.0004-0.11320.86080.10871.21310.0231-0.006-0.02530.03270.03930.0373-0.19810.0686-0.06240.0429-0.00160.01140.0132-0.0010.02261.339-4.1925.113
40.2752-0.1159-0.19840.85920.0851.1702-0.02270.02710.0674-0.0130.01820.0236-0.04610.05440.00460.0085-0.0117-0.01060.02260.00650.03032.53923.6057.779
539.26640-3.063568.484208.87-0.56441.4013-0.6081-0.94210.308-0.66280.21-0.66740.25630.3516-0.0659-0.01760.0905-0.03430.02591.067-9.116-2.857
60.1914-0.1473-0.3340.77630.19620.9601-0.0825-0.02220.0055-0.05870.01510.02470.17520.07290.06750.06030.0082-0.00280.01710.00460.01895.6999.0235.845
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A401 - 513
2X-RAY DIFFRACTION2A600 - 601
3X-RAY DIFFRACTION3A636 - 769
4X-RAY DIFFRACTION4B400 - 513
5X-RAY DIFFRACTION5B600 - 601
6X-RAY DIFFRACTION6B636 - 774

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