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- PDB-5l2e: Crystal structure of rat Glutamate receptor delta-2 extracellular... -

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Basic information

Entry
Database: PDB / ID: 5l2e
TitleCrystal structure of rat Glutamate receptor delta-2 extracellular domain
ComponentsGlutamate receptor ionotropic, delta-2,Glutamate receptor ionotropic, delta-2
KeywordsPROTEIN BINDING / Synapse Protein / Cell Surface Protein / Glycoprotein / Nervous System
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 / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / regulation of neuron projection development / parallel fiber to Purkinje cell synapse / 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 / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / regulation of neuron projection development / parallel fiber to Purkinje cell synapse / ionotropic glutamate receptor complex / regulation of presynapse assembly / regulation of postsynaptic membrane neurotransmitter receptor levels / prepulse inhibition / regulation of neuron apoptotic process / somatodendritic compartment / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / excitatory postsynaptic potential / synaptic transmission, glutamatergic / PDZ domain binding / modulation of chemical synaptic transmission / postsynaptic density membrane / protein localization / scaffold protein binding / postsynaptic membrane / dendritic spine / synapse / glutamatergic synapse / identical protein binding / membrane / 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 / Periplasmic binding protein-like I
Similarity search - Domain/homology
Glutamate receptor ionotropic, delta-2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.152 Å
AuthorsCheng, S. / Ozkan, E.
CitationJournal: Structure / Year: 2016
Title: Conformational Plasticity in the Transsynaptic Neurexin-Cerebellin-Glutamate Receptor Adhesion Complex.
Authors: Cheng, S. / Seven, A.B. / Wang, J. / Skiniotis, G. / Ozkan, E.
History
DepositionAug 1, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 28, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2023Group: 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 / pdbx_reflns_twin
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_reflns_twin.operator
Revision 1.2Oct 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,Glutamate receptor ionotropic, delta-2
B: Glutamate receptor ionotropic, delta-2,Glutamate receptor ionotropic, delta-2
C: Glutamate receptor ionotropic, delta-2,Glutamate receptor ionotropic, delta-2


Theoretical massNumber of molelcules
Total (without water)233,5013
Polymers233,5013
Non-polymers00
Water00
1
A: Glutamate receptor ionotropic, delta-2,Glutamate receptor ionotropic, delta-2

A: Glutamate receptor ionotropic, delta-2,Glutamate receptor ionotropic, delta-2


Theoretical massNumber of molelcules
Total (without water)155,6682
Polymers155,6682
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_467y-1,x+1,-z+21
Buried area3640 Å2
ΔGint-16 kcal/mol
Surface area58950 Å2
MethodPISA
2
B: Glutamate receptor ionotropic, delta-2,Glutamate receptor ionotropic, delta-2
C: Glutamate receptor ionotropic, delta-2,Glutamate receptor ionotropic, delta-2


Theoretical massNumber of molelcules
Total (without water)155,6682
Polymers155,6682
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3750 Å2
ΔGint-17 kcal/mol
Surface area58760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)179.172, 179.172, 214.390
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

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


Mass: 77833.812 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Grid2 / Cell line (production host): High Five (BTI-TN-5B1-4) / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q63226
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: 4.25 Å3/Da / Density % sol: 71.09 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 6.6
Details: 0.1 M Sodium cacodylate pH 6.6, 1.3 M Ammonium dihydrogen phosphate

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 19, 2016
RadiationMonochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
Reflection twinOperator: -h,-k,l / Fraction: 0.49
ReflectionResolution: 4.15→50 Å / Num. obs: 30494 / % possible obs: 100 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.157 / Rsym value: 0.157 / Net I/av σ(I): 8.9 / Net I/σ(I): 8.9
Reflection shellResolution: 4.15→4.22 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.795 / Mean I/σ(I) obs: 1.6 / CC1/2: 0.457 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(dev_2481: ???)refinement
HKL-20000.98.712data reduction
PHASER2.7.12phasing
Coot0.8.3model building
HKL-20000.98.712data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2VT3 and 5KC8

2vt3

5kc8


Resolution: 4.152→46.583 Å / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 24.5
Details: Refined with twin law -h,-k,l and twin fraction of 0.49.
RfactorNum. reflection% reflection
Rfree0.2604 1994 6.62 %
Rwork0.2112 --
obs0.2176 30109 98.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 4.152→46.583 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15408 0 0 0 15408
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00315717
X-RAY DIFFRACTIONf_angle_d0.61321294
X-RAY DIFFRACTIONf_dihedral_angle_d10.3959426
X-RAY DIFFRACTIONf_chiral_restr0.0462376
X-RAY DIFFRACTIONf_plane_restr0.0042760
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.1566-4.26040.27171230.21361764X-RAY DIFFRACTION82
4.2604-4.37550.26741310.19461970X-RAY DIFFRACTION92
4.3755-4.50420.29581390.1951972X-RAY DIFFRACTION93
4.5042-4.64940.29861400.19362004X-RAY DIFFRACTION93
4.6494-4.81540.23871400.18821998X-RAY DIFFRACTION93
4.8154-5.00790.23131390.18362008X-RAY DIFFRACTION93
5.0079-5.23550.24261410.19192012X-RAY DIFFRACTION93
5.2355-5.5110.23321420.21952012X-RAY DIFFRACTION93
5.511-5.85560.24521440.22862012X-RAY DIFFRACTION93
5.8556-6.30650.28791440.23032035X-RAY DIFFRACTION93
6.3065-6.93890.26751440.22932048X-RAY DIFFRACTION93
6.9389-7.93790.2441420.21552034X-RAY DIFFRACTION93
7.9379-9.98180.23811500.20962088X-RAY DIFFRACTION93
9.9818-44.10030.28191540.27952150X-RAY DIFFRACTION93

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