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- PDB-5kc8: Crystal structure of the amino-terminal domain (ATD) of iGluR Del... -

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Basic information

Entry
Database: PDB / ID: 5kc8
TitleCrystal structure of the amino-terminal domain (ATD) of iGluR Delta-2 (GluD2)
ComponentsGlutamate receptor ionotropic, delta-2
KeywordsSIGNALING PROTEIN / ionotropic glutamate receptor (iGluR) / neurotransmission
Function / homology
Function and homology information


trans-synaptic protein complex / cerebellar granule cell differentiation / positive regulation of long-term synaptic depression / excitatory synapse assembly / synaptic signaling via neuropeptide / regulation of postsynaptic density assembly / glutamate receptor activity / positive regulation of synapse assembly / heterophilic cell-cell adhesion / glutamate receptor signaling pathway ...trans-synaptic protein complex / cerebellar granule cell differentiation / positive regulation of long-term synaptic depression / excitatory synapse assembly / synaptic signaling via neuropeptide / regulation of postsynaptic density assembly / glutamate receptor activity / positive regulation of synapse assembly / heterophilic cell-cell adhesion / glutamate receptor signaling pathway / parallel fiber to Purkinje cell synapse / regulation of neuron projection development / AMPA glutamate receptor activity / AMPA glutamate receptor complex / ionotropic glutamate receptor complex / regulation of presynapse assembly / prepulse inhibition / regulation of postsynaptic membrane neurotransmitter receptor levels / regulation of neuron apoptotic process / excitatory postsynaptic potential / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / synaptic transmission, glutamatergic / PDZ domain binding / postsynaptic density membrane / modulation of chemical synaptic transmission / intracellular protein localization / scaffold protein binding / dendritic spine / synapse / glutamatergic synapse / metal ion binding / identical protein binding / plasma membrane
Similarity search - Function
Response regulator / 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 ...Response regulator / 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 I / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Glutamate receptor ionotropic, delta-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.751 Å
AuthorsElegheert, J. / Clay, J.E. / Siebold, C. / Aricescu, A.R.
CitationJournal: Science / Year: 2016
Title: Structural basis for integration of GluD receptors within synaptic organizer complexes.
Authors: Elegheert, J. / Kakegawa, W. / Clay, J.E. / Shanks, N.F. / Behiels, E. / Matsuda, K. / Kohda, K. / Miura, E. / Rossmann, M. / Mitakidis, N. / Motohashi, J. / Chang, V.T. / Siebold, C. / ...Authors: Elegheert, J. / Kakegawa, W. / Clay, J.E. / Shanks, N.F. / Behiels, E. / Matsuda, K. / Kohda, K. / Miura, E. / Rossmann, M. / Mitakidis, N. / Motohashi, J. / Chang, V.T. / Siebold, C. / Greger, I.H. / Nakagawa, T. / Yuzaki, M. / Aricescu, A.R.
History
DepositionJun 5, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jul 27, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 3, 2016Group: Structure summary
Revision 1.2Jan 10, 2024Group: 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
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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id
Revision 1.3Oct 23, 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, delta-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,7376
Polymers48,4711
Non-polymers2665
Water4,270237
1
A: Glutamate receptor ionotropic, delta-2
hetero molecules

A: Glutamate receptor ionotropic, delta-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,47412
Polymers96,9422
Non-polymers53310
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area4880 Å2
ΔGint-15 kcal/mol
Surface area33460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.100, 79.160, 246.690
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
SymmetryPoint symmetry: (Schoenflies symbol: C2 (2 fold cyclic))

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Components

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


Mass: 48470.797 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GRID2, GLURD2 / Plasmid: pHLsec / Cell line (production host): HEK293S / Production host: Homo sapiens (human) / References: UniProt: O43424
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 237 / 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: 2.27 Å3/Da / Density % sol: 45.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 20% (w/v) polyethylene glycol 1000, 0.2 M calcium Acetate, 0.1 M imidazole pH 8.0 and 0.4 M NDSB-221 (non-detergent sulfobetaine 221)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 27, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.75→57.03 Å / Num. obs: 44958 / % possible obs: 99.6 % / Redundancy: 15.3 % / Biso Wilson estimate: 25.6 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.078 / Net I/σ(I): 24.2
Reflection shellResolution: 1.75→1.8 Å / Redundancy: 9.5 % / Rmerge(I) obs: 1.314 / Mean I/σ(I) obs: 2.2 / % possible all: 98.3

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Processing

Software
NameVersionClassification
PHENIXdev_1772refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2WJW

2wjw


Resolution: 1.751→41.871 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2184 2242 4.99 %
Rwork0.1892 --
obs0.1907 44931 99.52 %
Solvent computationShrinkage radii: 1 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 41.8 Å2
Refinement stepCycle: LAST / Resolution: 1.751→41.871 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3143 0 14 237 3394
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083222
X-RAY DIFFRACTIONf_angle_d0.9174335
X-RAY DIFFRACTIONf_dihedral_angle_d12.4761190
X-RAY DIFFRACTIONf_chiral_restr0.037492
X-RAY DIFFRACTIONf_plane_restr0.005564
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7511-1.78910.3421240.30462595X-RAY DIFFRACTION98
1.7891-1.83080.31851390.2752593X-RAY DIFFRACTION99
1.8308-1.87650.31651320.26972656X-RAY DIFFRACTION99
1.8765-1.92730.27861370.24192589X-RAY DIFFRACTION99
1.9273-1.9840.27331450.23762636X-RAY DIFFRACTION100
1.984-2.0480.30931500.22452630X-RAY DIFFRACTION99
2.048-2.12120.26531380.22572643X-RAY DIFFRACTION100
2.1212-2.20620.24931620.21052605X-RAY DIFFRACTION100
2.2062-2.30660.22691430.19512675X-RAY DIFFRACTION100
2.3066-2.42810.21311440.1952650X-RAY DIFFRACTION100
2.4281-2.58030.2321350.19422666X-RAY DIFFRACTION100
2.5803-2.77940.22731310.18932697X-RAY DIFFRACTION100
2.7794-3.05910.1961460.1942706X-RAY DIFFRACTION100
3.0591-3.50150.23391260.18882733X-RAY DIFFRACTION100
3.5015-4.41080.18591470.15942735X-RAY DIFFRACTION100
4.4108-41.8830.17191430.15732880X-RAY DIFFRACTION100

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