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- PDB-3s2v: Crystal Structure of the Ligand Binding Domain of GluK1 in Comple... -

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Basic information

Entry
Database: PDB / ID: 3s2v
TitleCrystal Structure of the Ligand Binding Domain of GluK1 in Complex with an Antagonist (S)-1-(2'-Amino-2'-carboxyethyl)-3-[(2-carboxythien-3-yl)methyl]thieno[3,4-d]pyrimidin-2,4-dione at 2.5 A Resolution
ComponentsGlutamate receptor, ionotropic kainate 1
KeywordsMEMBRANE PROTEIN / antagonist / Ionotropic Glutamate Receptor
Function / homology
Function and homology information


negative regulation of synaptic transmission, GABAergic / gamma-aminobutyric acid secretion / L-glutamate transmembrane transporter activity / positive regulation of gamma-aminobutyric acid secretion / Activation of Na-permeable kainate receptors / kainate selective glutamate receptor complex / Activation of Ca-permeable Kainate Receptor / regulation of short-term neuronal synaptic plasticity / negative regulation of synaptic transmission, glutamatergic / inhibitory postsynaptic potential ...negative regulation of synaptic transmission, GABAergic / gamma-aminobutyric acid secretion / L-glutamate transmembrane transporter activity / positive regulation of gamma-aminobutyric acid secretion / Activation of Na-permeable kainate receptors / kainate selective glutamate receptor complex / Activation of Ca-permeable Kainate Receptor / regulation of short-term neuronal synaptic plasticity / negative regulation of synaptic transmission, glutamatergic / inhibitory postsynaptic potential / glutamate binding / synaptic transmission, GABAergic / adult behavior / modulation of excitatory postsynaptic potential / behavioral response to pain / kainate selective glutamate receptor activity / ionotropic glutamate receptor complex / extracellularly glutamate-gated ion channel activity / membrane depolarization / 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 / ionotropic glutamate receptor signaling pathway / SNARE binding / regulation of membrane potential / excitatory postsynaptic potential / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / positive regulation of synaptic transmission, GABAergic / synaptic transmission, glutamatergic / establishment of localization in cell / modulation of chemical synaptic transmission / postsynaptic density membrane / terminal bouton / regulation of synaptic plasticity / nervous system development / presynaptic membrane / scaffold protein binding / chemical synaptic transmission / postsynaptic membrane / receptor complex / postsynaptic density / neuronal cell body / synapse / dendrite / glutamatergic 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
Chem-3HU / Glutamate receptor ionotropic, kainate 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsVenskutonyte, R. / Frydenvang, K. / Kastrup, J.S.
Citation
Journal: J.Med.Chem. / Year: 2011
Title: Selective kainate receptor (GluK1) ligands structurally based upon 1H-cyclopentapyrimidin-2,4(1H,3H)-dione: synthesis, molecular modeling, and pharmacological and biostructural characterization.
Authors: Venskutonyte, R. / Butini, S. / Coccone, S.S. / Gemma, S. / Brindisi, M. / Kumar, V. / Guarino, E. / Maramai, S. / Valenti, S. / Amir, A. / Valades, E.A. / Frydenvang, K. / Kastrup, J.S. / ...Authors: Venskutonyte, R. / Butini, S. / Coccone, S.S. / Gemma, S. / Brindisi, M. / Kumar, V. / Guarino, E. / Maramai, S. / Valenti, S. / Amir, A. / Valades, E.A. / Frydenvang, K. / Kastrup, J.S. / Novellino, E. / Campiani, G. / Pickering, D.S.
#1: Journal: Febs Lett. / Year: 2005
Title: Crystal structure of the kainate receptor GluR5 ligand-binding core in complex with (S)-glutamate.
Authors: Naur, P. / Vestergaard, B. / Skov, L.K. / Egebjerg, J. / Gajhede, M. / Kastrup, J.S.
History
DepositionMay 17, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 22, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 23, 2012Group: Database references
Revision 1.3Aug 9, 2017Group: Data collection / Refinement description / Source and taxonomy
Category: diffrn_source / entity_src_gen / software / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.5Sep 13, 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
Revision 1.6Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)59,51610
Polymers58,2172
Non-polymers1,2998
Water5,945330
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3500 Å2
ΔGint-64 kcal/mol
Surface area23980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.459, 93.353, 107.171
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Glutamate receptor, ionotropic kainate 1


Mass: 29108.453 Da / Num. of mol.: 2 / Fragment: unp residues 430-544 AND 667-805
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: GRIK1 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): Origami 2 / References: UniProt: P22756

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Non-polymers , 5 types, 338 molecules

#2: Chemical ChemComp-3HU / (S)-1-(2'-AMINO-2'-CARBOXYETHYL)-3-[(2-CARBOXYTHIEN-3-YL)METHYL]THIENO[3,4-D]PYRIMIDIN-2,4-DIONE


Mass: 395.410 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H13N3O6S2
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 330 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Sequence detailsTHE STRUCTURE IS REPRESENTATIVE OF SEGMENTS S1 AND S2 COMPRISING THE LIGAND BINDING DOMAIN OF THE ...THE STRUCTURE IS REPRESENTATIVE OF SEGMENTS S1 AND S2 COMPRISING THE LIGAND BINDING DOMAIN OF THE FULL LENGTH GLUK1, CONNECTED WITH A GT LINKER. THEREFORE, SEQRES MATCHES DISCONTINUOUSLY WITH REFERENCE DATABASE (430-544, 667-805 OF ISOFORM GLUR5-2). DBREF RECORDS REFERS TO UNP ENTRY P22756-2 .

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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: 2.64 Å3/Da / Density % sol: 53.42 %
Crystal growTemperature: 279 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 24.4% PEG4000, 0.3 M lithium sulfate, 0.1 M phosphate-citrate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 279K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 21, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→29.3 Å / Num. obs: 21923 / % possible obs: 99.8 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.094 / Net I/σ(I): 5.6
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 1.8 / % possible all: 100

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Processing

Software
NameVersionClassification
MAR345data collection
PHASERphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2F34

2f34


Resolution: 2.5→19.779 Å / SU ML: 0.75 / Isotropic thermal model: Restrained / σ(F): 1.34 / Phase error: 24.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2565 1093 5 %
Rwork0.1778 --
obs0.1817 21844 99.64 %
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 27.306 Å2 / ksol: 0.349 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.303 Å2-0 Å20 Å2
2---0.7341 Å20 Å2
3---0.4311 Å2
Refinement stepCycle: LAST / Resolution: 2.5→19.779 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4067 0 80 330 4477
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084232
X-RAY DIFFRACTIONf_angle_d1.2415712
X-RAY DIFFRACTIONf_dihedral_angle_d16.171594
X-RAY DIFFRACTIONf_chiral_restr0.07621
X-RAY DIFFRACTIONf_plane_restr0.005716
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5001-2.61360.29521340.20542554X-RAY DIFFRACTION100
2.6136-2.75110.36261360.21682568X-RAY DIFFRACTION100
2.7511-2.92290.31111350.21292569X-RAY DIFFRACTION100
2.9229-3.14780.28391340.19152555X-RAY DIFFRACTION100
3.1478-3.4630.27091370.18542593X-RAY DIFFRACTION100
3.463-3.96060.25321360.17052585X-RAY DIFFRACTION100
3.9606-4.97680.20121380.13432623X-RAY DIFFRACTION99
4.9768-19.77980.21181430.17362704X-RAY DIFFRACTION98

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