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- PDB-4g8n: Crystal structure of the kainate receptor GluK3 ligand-binding do... -

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Basic information

Entry
Database: PDB / ID: 4g8n
TitleCrystal structure of the kainate receptor GluK3 ligand-binding domain in complex with the agonist G8M
ComponentsGlutamate receptor, ionotropic kainate 3
KeywordsMEMBRANE PROTEIN/Agonist / membrane protein / ionotropic glutamate receptor / ligand binding domain / agonist complex / MEMBRANE PROTEIN-Agonist complex
Function / homology
Function and homology information


Presynaptic function of Kainate receptors / cochlear hair cell ribbon synapse / adenylate cyclase inhibiting G protein-coupled glutamate receptor activity / kainate selective glutamate receptor complex / Activation of Ca-permeable Kainate Receptor / G protein-coupled glutamate receptor signaling pathway / glutamate receptor activity / negative regulation of synaptic transmission, glutamatergic / glutamate receptor signaling pathway / kainate selective glutamate receptor activity ...Presynaptic function of Kainate receptors / cochlear hair cell ribbon synapse / adenylate cyclase inhibiting G protein-coupled glutamate receptor activity / kainate selective glutamate receptor complex / Activation of Ca-permeable Kainate Receptor / G protein-coupled glutamate receptor signaling pathway / glutamate receptor activity / negative regulation of synaptic transmission, glutamatergic / glutamate receptor signaling pathway / kainate selective glutamate receptor activity / glutamate-gated receptor activity / glutamate-gated calcium ion channel activity / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / dendrite cytoplasm / regulation of membrane potential / 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 / dendrite / glutamatergic synapse / 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-G8M / : / Glutamate receptor ionotropic, kainate 3
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsVenskutonyte, R. / Kastrup, J.S. / Frydenvang, K. / Gajhede, M.
Citation
Journal: J.Struct.Biol. / Year: 2012
Title: Pharmacological and structural characterization of conformationally restricted (S)-glutamate analogues at ionotropic glutamate receptors.
Authors: Juknaite, L. / Venskutonyte, R. / Assaf, Z. / Faure, S. / Gefflaut, T. / Aitken, D.J. / Nielsen, B. / Gajhede, M. / Kastrup, J.S. / Bunch, L. / Frydenvang, K. / Pickering, D.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
DepositionJul 23, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 29, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 14, 2012Group: Database references
Revision 1.2Aug 23, 2017Group: Data collection / Refinement description / Source and taxonomy
Category: diffrn_source / entity_src_gen / software / Item: _diffrn_source.pdbx_synchrotron_site
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 / pdbx_struct_special_symmetry / 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
Revision 1.4Oct 30, 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 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,4156
Polymers29,0921
Non-polymers3225
Water2,324129
1
A: Glutamate receptor, ionotropic kainate 3
hetero molecules

A: Glutamate receptor, ionotropic kainate 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,82912
Polymers58,1852
Non-polymers64510
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555-x,y,-z1
Buried area2860 Å2
ΔGint-52 kcal/mol
Surface area22650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.821, 67.821, 122.881
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number91
Space group name H-MP4122
Components on special symmetry positions
IDModelComponents
11A-305-

K

21A-444-

HOH

31A-462-

HOH

41A-464-

HOH

51A-512-

HOH

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Components

#1: Protein Glutamate receptor, ionotropic kainate 3


Mass: 29092.453 Da / Num. of mol.: 1 / Fragment: UNP residues 432-546, 669-806
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: GRIK3 / Plasmid: pOPINJ / Production host: Escherichia coli (E. coli) / Strain (production host): Origami2 / References: UniProt: P42264
#2: Chemical ChemComp-G8M / (1S,2R)-2-[(S)-amino(carboxy)methyl]cyclobutanecarboxylic acid / (2S,1'R,2'S)-2-(2'-carboxycyclobutyl)glycine


Type: L-peptide linking / Mass: 173.167 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H11NO4
#3: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 129 / 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: 2.43 Å3/Da / Density % sol: 49.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 2.2M sodium/potassium phosphate. Crystals were grown in the presence of glutamate and soaked with new ligand G8M, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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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: Apr 15, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→67.821 Å / Num. all: 13403 / Num. obs: 13403 / % possible obs: 100 % / Redundancy: 7.9 % / Biso Wilson estimate: 31.1 Å2 / Rsym value: 0.078 / Net I/σ(I): 9.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.3-2.428.10.37821550919140.378100
2.42-2.578.10.2912.61448517920.291100
2.57-2.758.10.2133.51380317130.213100
2.75-2.978.10.1415.41277515860.141100
2.97-3.2580.0868.81187514890.086100
3.25-3.6480.05413.71064613370.054100
3.64-4.27.90.03918.4949312070.039100
4.2-5.147.70.03220.3792910300.032100
5.14-7.277.40.0361961928330.036100
7.27-29.6896.60.02621.633015020.02698.6

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Processing

Software
NameVersionClassificationNB
SCALA3.3.9data scaling
PHENIX1.7.3_928refinement
PDB_EXTRACT3.11data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3S9E

3s9e


Resolution: 2.3→29.689 Å / Occupancy max: 1 / Occupancy min: 0.47 / FOM work R set: 0.8552 / SU ML: 0.29 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 20.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2279 659 4.93 %RANDOM
Rwork0.1702 ---
obs0.1732 13368 100 %-
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.046 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso max: 106.07 Å2 / Biso mean: 28.617 Å2 / Biso min: 10.06 Å2
Baniso -1Baniso -2Baniso -3
1--0.1601 Å20 Å20 Å2
2---0.1601 Å20 Å2
3---0.3202 Å2
Refinement stepCycle: LAST / Resolution: 2.3→29.689 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2026 0 16 129 2171
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012100
X-RAY DIFFRACTIONf_angle_d1.0752813
X-RAY DIFFRACTIONf_chiral_restr0.073313
X-RAY DIFFRACTIONf_plane_restr0.004356
X-RAY DIFFRACTIONf_dihedral_angle_d13.838783
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection allNum. reflection obs
2.3-2.47750.26941410.1918245425952454
2.4775-2.72670.24361380.1832247926172479
2.7267-3.12090.23751130.1632252626392526
3.1209-3.93050.21681220.1566254826702548
3.9305-29.69120.21261450.1732270228472702

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