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- PDB-4mh5: Crystal structure of the kainate receptor GluK3 ligand binding do... -

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Basic information

Entry
Database: PDB / ID: 4mh5
TitleCrystal structure of the kainate receptor GluK3 ligand binding domain in complex with (S)-glutamate
ComponentsGlutamate receptor ionotropic, kainate 3
KeywordsReceptor/agonist / agonist / membrane / Receptor / Receptor-agonist complex
Function / homology
Function and homology information


Presynaptic function of Kainate receptors / regulation of presynaptic membrane potential / cochlear hair cell ribbon synapse / 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 activity / glutamate receptor signaling pathway ...Presynaptic function of Kainate receptors / regulation of presynaptic membrane potential / cochlear hair cell ribbon synapse / 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 activity / glutamate receptor signaling pathway / kainate selective glutamate receptor activity / glutamate-gated receptor 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 / monoatomic ion transmembrane transport / chemical synaptic transmission / perikaryon / postsynaptic membrane / axon / glutamatergic synapse / dendrite / 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
GLUTAMIC ACID / : / Glutamate receptor ionotropic, kainate 3
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.65 Å
AuthorsVenskutonyte, R. / Frydenvang, K. / Gajhede, M. / Kastrup, J.S.
CitationJournal: 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
DepositionAug 29, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 16, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 9, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 2.0Feb 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / database_2 / entity / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _atom_site.auth_comp_id / _atom_site.label_comp_id ..._atom_site.auth_comp_id / _atom_site.label_comp_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_label_comp_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _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_site.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.1Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)29,4817
Polymers29,0921
Non-polymers3886
Water5,242291
1
A: Glutamate receptor ionotropic, kainate 3
hetero molecules

A: Glutamate receptor ionotropic, kainate 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,96214
Polymers58,1852
Non-polymers77712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_455-x-1,y,-z1
Buried area4030 Å2
ΔGint-50 kcal/mol
Surface area23320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.800, 67.800, 122.430
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-302-

K

21A-429-

HOH

31A-524-

HOH

41A-532-

HOH

51A-595-

HOH

61A-605-

HOH

71A-635-

HOH

DetailsTHE BIOMOLECULE FORMS A DIMER IN THE CRYSTAL. HOWEVER, THIS DIMER IS MOST LIKELY NOT BIOLOGICALLY RELEVANT.

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Glutamate receptor ionotropic, kainate 3 / GluK3 / Glutamate receptor 7 / GluR-7 / GluR7


Mass: 29092.453 Da / Num. of mol.: 1 / Fragment: unp residues 432-546 and unp residues 669-806
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Grik3, Glur7 / Plasmid: pOPINJ / Production host: Escherichia coli (E. coli) / Strain (production host): Origami 2 / References: UniProt: P42264

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Non-polymers , 5 types, 297 molecules

#2: Chemical ChemComp-GLU / GLUTAMIC ACID


Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H9NO4
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 291 / Source method: isolated from a natural source / Formula: H2O

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Details

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). FIRST 3 RESIDUES OF THE STRUCTURE - GPG ARE CLONING REMNANTS.

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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: 2.42 Å3/Da / Density % sol: 49.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.2
Details: 1.8 M sodium/potassium phosphate, pH 8.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 18, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.65→27.897 Å / Num. all: 35179 / Num. obs: 35179 / % possible obs: 100 % / Redundancy: 7.8 % / Biso Wilson estimate: 16.15 Å2 / Rsym value: 0.068 / Net I/σ(I): 7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsRsym valueDiffraction-ID% possible all
1.65-1.747.40.37320.3731100
1.74-1.847.60.2453.10.2451100
1.84-1.977.80.1723.80.1721100
1.97-2.137.90.1135.40.1131100
2.13-2.3380.0797.60.0791100
2.33-2.6180.06410.70.0641100
2.61-3.0180.0678.80.0671100
3.01-3.697.90.0678.80.0671100
3.69-5.227.70.03515.60.0351100
5.22-27.89770.03314.60.033199.1

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 28.69 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å27.9 Å
Translation2.5 Å27.9 Å

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.16data scaling
PHASER2.1.4phasing
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.11data extraction
MAR345data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1YCJ

1ycj


Resolution: 1.65→27.897 Å / Occupancy max: 1 / Occupancy min: 0.35 / SU ML: 0.14 / σ(F): 0 / Phase error: 14.52 / Stereochemistry target values: ML
Details: The structure was refined with hydrogen atoms added and they were removed in the deposited pdb file.
RfactorNum. reflection% reflection
Rfree0.1814 1763 5.02 %
Rwork0.129 --
obs0.1317 35126 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.1234 Å2
Refinement stepCycle: LAST / Resolution: 1.65→27.897 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2030 0 20 291 2341
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012178
X-RAY DIFFRACTIONf_angle_d1.2712945
X-RAY DIFFRACTIONf_dihedral_angle_d13.534850
X-RAY DIFFRACTIONf_chiral_restr0.071325
X-RAY DIFFRACTIONf_plane_restr0.006374
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.69460.20951560.12642488X-RAY DIFFRACTION100
1.6946-1.74450.19171380.11942499X-RAY DIFFRACTION100
1.7445-1.80080.19981260.11012523X-RAY DIFFRACTION100
1.8008-1.86510.20191350.10582511X-RAY DIFFRACTION100
1.8651-1.93980.16091240.10282553X-RAY DIFFRACTION100
1.9398-2.0280.16381210.10512543X-RAY DIFFRACTION100
2.028-2.13490.19541370.10172549X-RAY DIFFRACTION100
2.1349-2.26860.15981340.10472539X-RAY DIFFRACTION100
2.2686-2.44370.18521260.11962578X-RAY DIFFRACTION100
2.4437-2.68940.17761440.13092565X-RAY DIFFRACTION100
2.6894-3.07820.17081470.13692581X-RAY DIFFRACTION100
3.0782-3.87650.17661440.13672629X-RAY DIFFRACTION100
3.8765-27.90060.19281310.15982805X-RAY DIFFRACTION100

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