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- PDB-5cc2: STRUCTURE OF THE LIGAND-BINDING DOMAIN OF THE IONOTROPIC GLUTAMAT... -

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Basic information

Entry
Database: PDB / ID: 5cc2
TitleSTRUCTURE OF THE LIGAND-BINDING DOMAIN OF THE IONOTROPIC GLUTAMATE RECEPTOR-LIKE GLUD2 IN COMPLEX WITH 7-CKA
ComponentsGlutamate receptor ionotropic, delta-2
KeywordsSIGNALING PROTEIN / Ionotropic glutamate receptor / GluD2 / ligand binding domain / NMDA receptor antagonist
Function / homology
Function and homology information


excitatory synapse assembly / cerebellar granule cell differentiation / positive regulation of long-term synaptic depression / regulation of postsynaptic density assembly / glutamate receptor activity / positive regulation of synapse assembly / parallel fiber to Purkinje cell synapse / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / regulation of neuron projection development / ionotropic glutamate receptor complex ...excitatory synapse assembly / cerebellar granule cell differentiation / positive regulation of long-term synaptic depression / regulation of postsynaptic density assembly / glutamate receptor activity / positive regulation of synapse assembly / parallel fiber to Purkinje cell synapse / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / regulation of neuron projection development / ionotropic glutamate receptor complex / regulation of presynapse assembly / prepulse inhibition / regulation of neuron apoptotic process / somatodendritic compartment / excitatory postsynaptic potential / synaptic transmission, glutamatergic / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / PDZ domain binding / postsynaptic density membrane / modulation of chemical synaptic transmission / protein localization / scaffold protein binding / postsynaptic membrane / dendritic spine / glutamatergic synapse / synapse / identical protein binding / membrane / 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
7-Chlorokynurenic acid / Glutamate receptor ionotropic, delta-2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.501 Å
AuthorsNaur, P. / Gajhede, M. / Kastrup, J.S.
Citation
Journal: Mol.Pharmacol. / Year: 2016
Title: Pharmacology and Structural Analysis of Ligand Binding to the Orthosteric Site of Glutamate-Like GluD2 Receptors.
Authors: Kristensen, A.S. / Hansen, K.B. / Naur, P. / Olsen, L. / Kurtkaya, N.L. / Dravid, S.M. / Kvist, T. / Yi, F. / Phlsgaard, J. / Clausen, R.P. / Gajhede, M. / Kastrup, J.S. / Traynelis, S.F.
History
DepositionJul 1, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Dec 30, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 20, 2016Group: Database references
Revision 1.2Jan 17, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Jan 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

Downloads & links

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Assembly

Deposited unit
A: Glutamate receptor ionotropic, delta-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,7366
Polymers29,9381
Non-polymers7985
Water43224
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area380 Å2
ΔGint-8 kcal/mol
Surface area12980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.210, 70.210, 134.500
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-303-

CKA

21A-303-

CKA

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Components

#1: Protein Glutamate receptor ionotropic, delta-2 / GluR delta-2 subunit


Mass: 29937.670 Da / Num. of mol.: 1 / Fragment: UNP residues 441-551,UNP residues 664-813
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Grid2 / Plasmid: PET28 / Production host: Escherichia coli K-12 (bacteria) / Variant (production host): ORIGAMI 2 / References: UniProt: Q63226
#2: Chemical ChemComp-CKA / 7-Chlorokynurenic acid / 7-CKA


Mass: 223.613 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H6ClNO3 / Comment: antidepressant, antagonist*YM
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 24 / 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: 2.77 Å3/Da / Density % sol: 55.57 %
Crystal growTemperature: 280 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 20 mM Hepes, 10 mm NaCl, 1 mM EDTA

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-2 / Wavelength: 1.0408 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Nov 22, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0408 Å / Relative weight: 1
ReflectionResolution: 2.501→30.58 Å / Num. all: 12222 / Num. obs: 12222 / % possible obs: 99.6 % / Redundancy: 5.1 % / Biso Wilson estimate: 53.18 Å2 / Rpim(I) all: 0.035 / Rrim(I) all: 0.08 / Rsym value: 0.072 / Net I/av σ(I): 8.231 / Net I/σ(I): 13.4 / Num. measured all: 62324
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
2.5-2.645.20.5191.5904517350.2510.5192.8100
2.64-2.85.20.3892865916570.1880.3893.9100
2.8-2.995.20.2123.7813215630.1020.2126.5100
2.99-3.235.20.1246759414620.0590.12410.3100
3.23-3.545.20.088.9701013600.0380.0815.5100
3.54-3.955.10.05512626512210.0260.05520.8100
3.95-4.575.10.04613.6558511020.0220.04624.6100
4.57-5.5950.05810.647839610.0280.05825.8100
5.59-7.914.80.04414.136527590.0220.04424.4100
7.91-30.5840.03319.215994020.0180.03326.487.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIXrefinement
MOSFLMdata reduction
SCALA3.3.9data scaling
PHASERphasing
PDB_EXTRACT3.15data extraction
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2V3T, molA

2v3t


Resolution: 2.501→30.577 Å / FOM work R set: 0.8074 / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 24.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2393 581 4.77 %Random selection
Rwork0.1928 11591 --
obs0.1951 12172 99.49 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 120.97 Å2 / Biso mean: 52.84 Å2 / Biso min: 14.3 Å2
Refinement stepCycle: final / Resolution: 2.501→30.577 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2048 0 52 24 2124
Biso mean--44.56 44.47 -
Num. residues----256
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032149
X-RAY DIFFRACTIONf_angle_d0.6562921
X-RAY DIFFRACTIONf_chiral_restr0.045308
X-RAY DIFFRACTIONf_plane_restr0.003375
X-RAY DIFFRACTIONf_dihedral_angle_d12.711769
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.501-2.7520.34751530.26752822X-RAY DIFFRACTION100
2.752-3.150.32981260.24272869X-RAY DIFFRACTION100
3.15-3.9670.25241520.18782895X-RAY DIFFRACTION100
3.967-30.5770.1871500.16683005X-RAY DIFFRACTION98
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)
12.19862.52650.29665.37040.41.1373-0.17010.15420.11340.02750.29940.0664-0.0678-0.0312-0.1250.27540.03760.01790.33290.0540.174615.56018.818825.6759
29.0362-3.88422.46116.0417-3.25382.96150.07860.1126-0.5909-0.39320.18130.65560.593-0.22-0.22130.3296-0.06850.04320.2937-0.00230.24874.2652-7.021321.3913
31.20492.4903-0.56137.52960.37451.373-0.4030.43140.0211-1.08650.5442-0.3893-0.12670.1571-0.11410.3557-0.05140.01180.49060.00530.293522.94237.357819.1918
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 148 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 149 through 188 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 189 through 258 )A0

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