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- PDB-2znt: Crystal structure of the ligand-binding core of the human ionotro... -

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Basic information

Entry
Database: PDB / ID: 2znt
TitleCrystal structure of the ligand-binding core of the human ionotropic glutamate receptor, GluR5, in complex with a novel selective agonist, dysiherbaine
ComponentsGlutamate receptor, ionotropic kainate 1
KeywordsMEMBRANE PROTEIN / GluR5 / kainate receptor / ligand-binding core / amino acid / agonist / dysiherbaine / Alternative splicing / Cell junction / Glycoprotein / Ion transport / Ionic channel / Membrane / Phosphoprotein / Polymorphism / Postsynaptic cell membrane / RNA editing / Synapse / Transmembrane / Transport
Function / homology
Function and homology information


Activation of Na-permeable kainate receptors / kainate selective glutamate receptor complex / glutamate receptor signaling pathway / Activation of Ca-permeable Kainate Receptor / kainate selective glutamate receptor activity / glutamate-gated receptor activity / glutamate-gated calcium ion channel activity / regulation of synaptic transmission, glutamatergic / synaptic transmission, glutamatergic / central nervous system development ...Activation of Na-permeable kainate receptors / kainate selective glutamate receptor complex / glutamate receptor signaling pathway / Activation of Ca-permeable Kainate Receptor / kainate selective glutamate receptor activity / glutamate-gated receptor activity / glutamate-gated calcium ion channel activity / regulation of synaptic transmission, glutamatergic / synaptic transmission, glutamatergic / central nervous system development / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / postsynaptic density membrane / modulation of chemical synaptic transmission / presynaptic membrane / nervous system development / chemical synaptic transmission / intracellular membrane-bounded organelle / 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
BETA-MERCAPTOETHANOL / Chem-DYH / Glutamate receptor ionotropic, kainate 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 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
DepositionMay 1, 2008Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 5, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 26, 2011Group: Database references
Revision 1.3Aug 16, 2017Group: Source and taxonomy / Category: entity_src_gen
Revision 1.4Nov 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_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_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

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Assembly

Deposited unit
A: Glutamate receptor, ionotropic kainate 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7887
Polymers29,0931
Non-polymers6956
Water4,053225
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)118.851, 65.137, 50.059
Angle α, β, γ (deg.)90.00, 107.03, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Glutamate receptor, ionotropic kainate 1 / Glutamate receptor 5 / GluR-5 / GluR5 / Excitatory amino acid receptor 3 / EAA3 / GluR5 ligand-binding core


Mass: 29093.441 Da / Num. of mol.: 1
Fragment: ligand-binding domain, UNP residues 445-559, UNP residues 682-820
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GRIK1, GLUR5 / Plasmid: pCold-I DNA / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P39086
#2: Chemical ChemComp-DYH / (2R,3aR,6S,7R,7aR)-2-[(2S)-2-amino-2-carboxyethyl]-6-hydroxy-7-(methylamino)hexahydro-2H-furo[3,2-b]pyran-2-carboxylic acid


Mass: 304.296 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H20N2O7
#3: Chemical
ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6OS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 225 / 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: 3.18 Å3/Da / Density % sol: 61.37 %
Crystal growTemperature: 279 K / Method: vapor diffusion, hanging drop / pH: 4.8
Details: PEG3350, NaCl, EDTA, pH4.8, VAPOR DIFFUSION, HANGING DROP, temperature 279K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Oct 11, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 46169 / % possible obs: 96.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rsym value: 0.044 / Net I/σ(I): 36.9
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 2.27 / Num. unique all: 3692 / Rsym value: 0.239 / % possible all: 76.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2ZNS

2zns


Resolution: 1.6→30 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.945 / SU B: 2.936 / SU ML: 0.053 / Cross valid method: THROUGHOUT / ESU R: 0.087 / ESU R Free: 0.087 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22538 2307 5 %RANDOM
Rwork0.19895 ---
obs0.20029 43859 96.01 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.956 Å2
Baniso -1Baniso -2Baniso -3
1-0.25 Å20 Å2-0.64 Å2
2--0.96 Å20 Å2
3----1.58 Å2
Refinement stepCycle: LAST / Resolution: 1.6→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2131 0 41 225 2397
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0222208
X-RAY DIFFRACTIONr_angle_refined_deg1.3371.9892972
X-RAY DIFFRACTIONr_dihedral_angle_1_deg11.1335254
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.38223.83899
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.30115436
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.5631516
X-RAY DIFFRACTIONr_chiral_restr0.0970.2340
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021579
X-RAY DIFFRACTIONr_nbd_refined0.2040.21084
X-RAY DIFFRACTIONr_nbtor_refined0.3060.21560
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1090.2180
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1860.227
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1160.28
X-RAY DIFFRACTIONr_mcbond_it0.811.51328
X-RAY DIFFRACTIONr_mcangle_it1.21522105
X-RAY DIFFRACTIONr_scbond_it1.7731004
X-RAY DIFFRACTIONr_scangle_it2.6684.5867
LS refinement shellResolution: 1.602→1.644 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.331 140 -
Rwork0.302 2405 -
obs--71.77 %
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)
11.27860.461-0.13911.39390.00561.0336-0.0106-0.034-0.0108-0.0390.0141-0.0275-0.0410.1271-0.0035-0.07030.0099-0.0087-0.053-0.0136-0.092619.4605-0.986713.1594
20.3359-1.31021.54745.1108-6.0367.12870.27140.2042-0.24550.2601-0.1834-0.38890.3842-0.154-0.0880.0511-0.0930.01710.0307-0.02550.018623.0293-1.135112.7982
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA415 - 7891 - 255
2X-RAY DIFFRACTION2AB11

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