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- PDB-5ikb: Crystal structure of the kainate receptor GluK4 ligand binding do... -

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Basic information

Entry
Database: PDB / ID: 5ikb
TitleCrystal structure of the kainate receptor GluK4 ligand binding domain in complex with kainate
ComponentsGlutamate receptor ionotropic, kainate 4,Glutamate receptor ionotropic, kainate 4
KeywordsMEMBRANE PROTEIN / high-affinity kainate receptor / ligand binding domain / ion channel
Function / homology
Function and homology information


kainate selective glutamate receptor complex / Activation of Ca-permeable Kainate Receptor / kainate selective glutamate receptor activity / ionotropic glutamate receptor complex / glutamate-gated receptor activity / monoatomic ion transport / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / hippocampal mossy fiber to CA3 synapse / synaptic transmission, glutamatergic / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential ...kainate selective glutamate receptor complex / Activation of Ca-permeable Kainate Receptor / kainate selective glutamate receptor activity / ionotropic glutamate receptor complex / glutamate-gated receptor activity / monoatomic ion transport / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / hippocampal mossy fiber to CA3 synapse / synaptic transmission, glutamatergic / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / postsynaptic density membrane / modulation of chemical synaptic transmission / terminal bouton / presynaptic membrane / chemical synaptic transmission / perikaryon / postsynaptic membrane / axon / glutamatergic synapse / dendrite / synapse / 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
3-(CARBOXYMETHYL)-4-ISOPROPENYLPROLINE / Glutamate receptor ionotropic, kainate 4
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsKristensen, O. / Kristensen, L.B. / Frydenvang, K. / Kastrup, J.S.
Funding support Denmark, 2items
OrganizationGrant numberCountry
The Lundbeck Foundation Denmark
E.C. (FP7)Biostruct-X
CitationJournal: Structure / Year: 2016
Title: The Structure of a High-Affinity Kainate Receptor: GluK4 Ligand-Binding Domain Crystallized with Kainate.
Authors: Kristensen, O. / Kristensen, L.B. / Mollerud, S. / Frydenvang, K. / Pickering, D.S. / Kastrup, J.S.
History
DepositionMar 3, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Aug 24, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 14, 2016Group: Database references
Revision 1.2Aug 9, 2017Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 2.0Mar 27, 2019Group: Atomic model / Data collection / Source and taxonomy / Category: atom_site / entity_src_gen
Item: _atom_site.occupancy / _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_strain
Revision 2.1Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glutamate receptor ionotropic, kainate 4,Glutamate receptor ionotropic, kainate 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5694
Polymers29,1711
Non-polymers3973
Water3,963220
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area510 Å2
ΔGint1 kcal/mol
Surface area12190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.500, 69.870, 162.760
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-463-

HOH

21A-574-

HOH

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Components

#1: Protein Glutamate receptor ionotropic, kainate 4,Glutamate receptor ionotropic, kainate 4 / GluK4 / Glutamate receptor KA-1 / KA1


Mass: 29171.211 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Grik4 / Plasmid: pPEU6 / Cell line (production host): High Five / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q01812
#2: Chemical ChemComp-KAI / 3-(CARBOXYMETHYL)-4-ISOPROPENYLPROLINE / KAINATE


Mass: 213.230 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15NO4 / Comment: neurotransmitter, agonist*YM
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 220 / 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: 2.2 Å3/Da / Density % sol: 43.7 % / Description: Needle cluster
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 15 % glycerol, 25.5 % PEG4000, 0.17 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.966 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Oct 7, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
ReflectionResolution: 2.05→40.69 Å / Num. obs: 16260 / % possible obs: 99.3 % / Redundancy: 5.8 % / Biso Wilson estimate: 23.95 Å2 / Rmerge(I) obs: 0.136 / Net I/σ(I): 8.9
Reflection shellResolution: 2.05→2.1 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.709 / Mean I/σ(I) obs: 2 / % possible all: 96.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
PHENIX1.10.1refinement
xia23.6.3data reduction
XDSMarch 1, 2015data reduction
PHASER2.6.0phasing
Coot0.8.2model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2XXT

2xxt


Resolution: 2.05→40.69 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.879 / SU B: 5.919 / SU ML: 0.158 / Cross valid method: THROUGHOUT / ESU R: 0.244 / ESU R Free: 0.212 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2617 897 5.5 %RANDOM
Rwork0.19099 ---
obs0.19494 15326 99.11 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 26.711 Å2
Baniso -1Baniso -2Baniso -3
1-0.21 Å20 Å2-0 Å2
2--0.08 Å20 Å2
3----0.29 Å2
Refinement stepCycle: LAST / Resolution: 2.05→40.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1995 0 27 220 2242
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0192116
X-RAY DIFFRACTIONr_bond_other_d0.0020.021993
X-RAY DIFFRACTIONr_angle_refined_deg1.8051.9632866
X-RAY DIFFRACTIONr_angle_other_deg1.07834583
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3325262
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.14424.257101
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.39815370
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3751514
X-RAY DIFFRACTIONr_chiral_restr0.1130.2314
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022427
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02501
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_it2.1312.4161033
X-RAY DIFFRACTIONr_mcbond_other2.1312.4161033
X-RAY DIFFRACTIONr_mcangle_it3.2513.6081300
X-RAY DIFFRACTIONr_mcangle_other3.2493.6081301
X-RAY DIFFRACTIONr_scbond_it2.9192.8071083
X-RAY DIFFRACTIONr_scbond_other2.9142.8081083
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.5764.0711567
X-RAY DIFFRACTIONr_long_range_B_refined6.89920.3332531
X-RAY DIFFRACTIONr_long_range_B_other6.72920.0322461
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.05→2.103 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.342 58 -
Rwork0.241 1068 -
obs--95.99 %

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