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- PDB-5kca: Crystal structure of the Cbln1 C1q domain trimer in complex with ... -

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Basic information

Entry
Database: PDB / ID: 5kca
TitleCrystal structure of the Cbln1 C1q domain trimer in complex with the amino-terminal domain (ATD) of iGluR Delta-2 (GluD2)
ComponentsCerebellin-1,Cerebellin-1,Cerebellin-1,Glutamate receptor ionotropic, delta-2
KeywordsSIGNALING PROTEIN / Cerebellin / ionotropic glutamate receptor (iGluR) / neurotransmission
Function / homology
Function and homology information


negative regulation of inhibitory synapse assembly / trans-synaptic signaling, modulating synaptic transmission / trans-synaptic protein complex / cerebellar granule cell differentiation / positive regulation of long-term synaptic depression / excitatory synapse assembly / synaptic signaling via neuropeptide / maintenance of synapse structure / negative regulation of excitatory postsynaptic potential / regulation of postsynaptic density assembly ...negative regulation of inhibitory synapse assembly / trans-synaptic signaling, modulating synaptic transmission / trans-synaptic protein complex / cerebellar granule cell differentiation / positive regulation of long-term synaptic depression / excitatory synapse assembly / synaptic signaling via neuropeptide / maintenance of synapse structure / negative regulation of excitatory postsynaptic potential / 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 / protein secretion / ionotropic glutamate receptor complex / regulation of presynapse assembly / synaptic cleft / prepulse inhibition / regulation of postsynaptic membrane neurotransmitter receptor levels / synapse assembly / 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 / establishment of localization in cell / postsynaptic density membrane / synapse organization / modulation of chemical synaptic transmission / intracellular protein localization / nervous system development / : / scaffold protein binding / chemical synaptic transmission / dendritic spine / postsynaptic membrane / synapse / glutamatergic synapse / extracellular region / metal ion binding / identical protein binding / plasma membrane
Similarity search - Function
: / C1q domain / C1q domain / C1q domain profile. / Complement component C1q domain. / Tumour necrosis factor-like domain superfamily / 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 ...: / C1q domain / C1q domain / C1q domain profile. / Complement component C1q domain. / Tumour necrosis factor-like domain superfamily / 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 / Cerebellin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsElegheert, J. / 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 1.1Jan 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
Revision 1.2Oct 9, 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: Cerebellin-1,Cerebellin-1,Cerebellin-1,Glutamate receptor ionotropic, delta-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,2782
Polymers97,2381
Non-polymers401
Water00
1
A: Cerebellin-1,Cerebellin-1,Cerebellin-1,Glutamate receptor ionotropic, delta-2
hetero molecules

A: Cerebellin-1,Cerebellin-1,Cerebellin-1,Glutamate receptor ionotropic, delta-2
hetero molecules

A: Cerebellin-1,Cerebellin-1,Cerebellin-1,Glutamate receptor ionotropic, delta-2
hetero molecules

A: Cerebellin-1,Cerebellin-1,Cerebellin-1,Glutamate receptor ionotropic, delta-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)389,1118
Polymers388,9514
Non-polymers1604
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554y,-x+y,z-1/61
crystal symmetry operation8_555x-y,-y,-z1
crystal symmetry operation12_555x,x-y,-z+1/61
Unit cell
Length a, b, c (Å)142.680, 142.680, 276.140
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
SymmetryPoint symmetry: (Schoenflies symbol: C2 (2 fold cyclic))

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Components

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


Mass: 97237.703 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CBLN1, GRID2, GLURD2 / Plasmid: pHLsec / Cell line (production host): HEK293S / Production host: Homo sapiens (human) / References: UniProt: P23435, UniProt: O43424
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 4.17 Å3/Da / Density % sol: 70.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 60% (v/v) tacsimate pH 7.0 (1.8305 M malonic acid, 0.25 M ammonium citrate tribasic, 0.12 M succinic acid, 0.3 M DL-malic acid, 0.4 M sodium acetate trihydrate, 0.5 M sodium formate, and 0. ...Details: 60% (v/v) tacsimate pH 7.0 (1.8305 M malonic acid, 0.25 M ammonium citrate tribasic, 0.12 M succinic acid, 0.3 M DL-malic acid, 0.4 M sodium acetate trihydrate, 0.5 M sodium formate, and 0.16 M ammonium tartrate dibasic)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.96862 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 10, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96862 Å / Relative weight: 1
ReflectionResolution: 3.1→46.05 Å / Num. obs: 30725 / % possible obs: 99.6 % / Redundancy: 7.6 % / Biso Wilson estimate: 66.4 Å2 / CC1/2: 0.986 / Rmerge(I) obs: 0.224 / Net I/σ(I): 9.5
Reflection shellResolution: 3.1→3.18 Å / Redundancy: 7.5 % / Rmerge(I) obs: 1.377 / Mean I/σ(I) obs: 1.5 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIXdev_1772refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5KC5, 5KC8

5kc5

5kc8


Resolution: 3.1→46.023 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2308 1545 5.03 %
Rwork0.2044 --
obs0.2057 30716 99.4 %
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 62.9 Å2
Refinement stepCycle: LAST / Resolution: 3.1→46.023 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6321 0 1 0 6322
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0056463
X-RAY DIFFRACTIONf_angle_d0.9668744
X-RAY DIFFRACTIONf_dihedral_angle_d14.4132332
X-RAY DIFFRACTIONf_chiral_restr0.039972
X-RAY DIFFRACTIONf_plane_restr0.0041136
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1001-3.20010.39051250.32822588X-RAY DIFFRACTION100
3.2001-3.31450.33831460.29622599X-RAY DIFFRACTION100
3.3145-3.44710.27521280.27082615X-RAY DIFFRACTION100
3.4471-3.6040.26371530.24422604X-RAY DIFFRACTION100
3.604-3.79390.25081450.21682621X-RAY DIFFRACTION100
3.7939-4.03150.22481320.19642639X-RAY DIFFRACTION100
4.0315-4.34250.23161340.18122641X-RAY DIFFRACTION100
4.3425-4.77910.18421550.15672654X-RAY DIFFRACTION100
4.7791-5.46970.16491450.16332669X-RAY DIFFRACTION100
5.4697-6.88750.22961380.20082716X-RAY DIFFRACTION99
6.8875-46.02840.21751440.192825X-RAY DIFFRACTION97

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