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- PDB-4e0w: Crystal structure of the kainate receptor GluK3 ligand binding do... -

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Basic information

Entry
Database: PDB / ID: 4e0w
TitleCrystal structure of the kainate receptor GluK3 ligand binding domain in complex with kainate
ComponentsGlutamate receptor, ionotropic kainate 3
KeywordsMEMBRANE PROTEIN / ionotropic glutamate receptor / GluK3 / ligand-binding domain / agonist
Function / homology
Function and homology information


Presynaptic function of Kainate receptors / adenylate cyclase inhibiting G protein-coupled glutamate receptor activity / kainate selective glutamate receptor complex / G protein-coupled glutamate receptor signaling pathway / Activation of Ca-permeable Kainate Receptor / negative regulation of synaptic transmission, glutamatergic / glutamate receptor signaling pathway / glutamate receptor activity / kainate selective glutamate receptor activity / glutamate-gated receptor activity ...Presynaptic function of Kainate receptors / adenylate cyclase inhibiting G protein-coupled glutamate receptor activity / kainate selective glutamate receptor complex / G protein-coupled glutamate receptor signaling pathway / Activation of Ca-permeable Kainate Receptor / negative regulation of synaptic transmission, glutamatergic / glutamate receptor signaling pathway / glutamate receptor activity / kainate selective glutamate receptor activity / glutamate-gated receptor activity / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / dendrite cytoplasm / synaptic transmission, glutamatergic / regulation of membrane potential / 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 / axon / glutamatergic synapse / dendrite / 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
: / 3-(CARBOXYMETHYL)-4-ISOPROPENYLPROLINE / Glutamate receptor ionotropic, kainate 3
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3501 Å
AuthorsVenskutonyte, R. / Frydenvang, K. / Kastrup, J.S.
Citation
Journal: Neurochem Int / Year: 2012
Title: Kainate induces various domain closures in AMPA and kainate receptors.
Authors: Venskutonyte, R. / Frydenvang, K. / Hald, H. / Rabassa, A.C. / Gajhede, M. / Ahring, P.K. / Kastrup, J.S.
#1: Journal: J.Struct.Biol. / Year: 2011
Title: Binding site and interlobe interactions of the ionotropic glutamate receptor GluK3 ligand binding domain revealed by high resolution crystal structure in complex with (S)-glutamate.
Authors: Venskutonyte, R. / Frydenvang, K. / Gajhede, M. / Bunch, L. / Pickering, D.S. / Kastrup, J.S.
History
DepositionMar 5, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 2, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 19, 2012Group: Database references
Revision 1.2Aug 2, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.3Sep 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 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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

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Assembly

Deposited unit
A: Glutamate receptor, ionotropic kainate 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,4556
Polymers29,0921
Non-polymers3625
Water2,000111
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)68.558, 68.558, 126.883
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number91
Space group name H-MP4122
Components on special symmetry positions
IDModelComponents
11A-305-

K

21A-493-

HOH

DetailsA tetrameric multimer representing the known biologically significant oligomerization state of the molecule cannot be generated by symmetry within the crystal.

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Components

#1: Protein Glutamate receptor, ionotropic kainate 3 / / Glutamate receptor 7 / GluR-7 / GluR7


Mass: 29092.453 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Glur7, Grik3 / Plasmid: pOPINJ / Production host: Escherichia coli (E. coli) / Strain (production host): Origami 2 / References: UniProt: P42264
#2: Chemical ChemComp-KAI / 3-(CARBOXYMETHYL)-4-ISOPROPENYLPROLINE / KAINATE / Kainic acid


Mass: 213.230 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15NO4 / Comment: neurotransmitter, agonist*YM
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 111 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE PROTEIN CRYSTALLIZED IS THE EXTRACELLULAR LIGAND BINDING DOMAIN OF GLUK3. TRANSMEMBRANE REGIONS ...THE PROTEIN CRYSTALLIZED IS THE EXTRACELLULAR LIGAND BINDING DOMAIN OF GLUK3. TRANSMEMBRANE REGIONS WERE GENETICALLY REMOVED AND REPLACED WITH A GLY-THR LINKER (RESIDUES 119 AND 120 OF THE STRUCTURE). THEREFORE, THE SEQUENCE MATCHES DISCONTINUOUSLY WITH THE REFERENCE DATABASE (432-546, 669-806)

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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: 2.56 Å3/Da / Density % sol: 52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.2
Details: 1.8 M SODIUM/POTASSIUM PHOSPHATE, CRYSTALS GROWN IN PRESENCE OF GLUTAMATE SOAKED WITH KAINATE, pH 8.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 26, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 2.35→48.478 Å / Num. all: 13287 / Num. obs: 13274 / % possible obs: 100 % / Redundancy: 7.9 % / Biso Wilson estimate: 36.4 Å2 / Rsym value: 0.075 / Net I/σ(I): 9.7
Reflection shellResolution: 2.35→2.48 Å / Redundancy: 8.2 % / Rmerge(I) obs: 0.393 / Mean I/σ(I) obs: 2 / Rsym value: 0.393 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.16data scaling
PHASERphasing
PHENIX1.7.3_928refinement
PDB_EXTRACT3.1data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3S9E

3s9e


Resolution: 2.3501→48.478 Å / Occupancy max: 1 / Occupancy min: 0.38 / SU ML: 0.28 / Isotropic thermal model: Isotropic / σ(F): 1.38 / Phase error: 21.05 / Stereochemistry target values: ML
Details: RESIDUES 1-4 (GPGT) WERE NOT LOCATED IN THE ELECTRON DENSITY MAP.
RfactorNum. reflection% reflection
Rfree0.2322 655 4.95 %
Rwork0.179 --
obs0.1816 13243 99.98 %
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.155 Å2 / ksol: 0.378 e/Å3
Displacement parametersBiso mean: 41.9 Å2
Baniso -1Baniso -2Baniso -3
1--0.8275 Å2-0 Å20 Å2
2---0.8275 Å20 Å2
3---1.655 Å2
Refinement stepCycle: LAST / Resolution: 2.3501→48.478 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2019 0 19 111 2149
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0122110
X-RAY DIFFRACTIONf_angle_d1.0622829
X-RAY DIFFRACTIONf_dihedral_angle_d15.389795
X-RAY DIFFRACTIONf_chiral_restr0.072313
X-RAY DIFFRACTIONf_plane_restr0.004358
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3501-2.53150.28591500.20412432X-RAY DIFFRACTION100
2.5315-2.78630.27831180.20622462X-RAY DIFFRACTION100
2.7863-3.18940.27961300.18682482X-RAY DIFFRACTION100
3.1894-4.0180.19431270.17112530X-RAY DIFFRACTION100
4.018-48.48810.21061300.16652682X-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)
11.9789-1.0342-0.10351.66970.27314.13220.08280.1122-0.0206-0.24380.0499-0.02760.17390.1347-0.11010.1223-0.0038-0.04290.10230.0120.1157-12.885744.1079-21.194
20.86990.22280.0070.75230.66660.83960.0156-0.0084-0.36950.35660.2205-0.54760.4880.4039-0.03340.22450.2222-0.20630.1228-0.05780.293-2.398326.2034-14.5059
34.26884.68710.62795.56650.24753.41080.0324-0.52040.47850.38560.00050.0752-0.1814-0.1286-0.03480.2730.0899-0.12260.2589-0.10070.2101-11.216946.2037-2.6061
40.8677-1.7205-0.37083.45570.61840.47930.00450.0151-0.42810.6154-0.06310.85270.7162-0.41880.22280.3054-0.12-0.00340.22510.02350.2494-22.533231.7921-13.0781
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 5:49)
2X-RAY DIFFRACTION2chain 'A' and (resseq 50:225)
3X-RAY DIFFRACTION3chain 'A' and (resseq 226:241)
4X-RAY DIFFRACTION4chain 'A' and (resseq 242:258)

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