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- PDB-5kc6: Crystal structure of Cbln1 (Val55-Gly58 deletion mutant) -

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Basic information

Entry
Database: PDB / ID: 5kc6
TitleCrystal structure of Cbln1 (Val55-Gly58 deletion mutant)
ComponentsCerebellin-1
KeywordsSIGNALING PROTEIN / Cerebellin / neurotransmission
Function / homology
Function and homology information


negative regulation of inhibitory synapse assembly / cerebellar granule cell differentiation / positive regulation of long-term synaptic depression / maintenance of synapse structure / regulation of postsynaptic density assembly / negative regulation of excitatory postsynaptic potential / positive regulation of synapse assembly / parallel fiber to Purkinje cell synapse / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / regulation of presynapse assembly ...negative regulation of inhibitory synapse assembly / cerebellar granule cell differentiation / positive regulation of long-term synaptic depression / maintenance of synapse structure / regulation of postsynaptic density assembly / negative regulation of excitatory postsynaptic potential / positive regulation of synapse assembly / parallel fiber to Purkinje cell synapse / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / regulation of presynapse assembly / protein secretion / synaptic cleft / synapse assembly / establishment of localization in cell / synapse organization / nervous system development / chemical synaptic transmission / postsynaptic membrane / collagen-containing extracellular matrix / glutamatergic synapse / extracellular region / identical protein binding
Similarity search - Function
C1q domain / C1q domain / C1q domain profile. / Complement component C1q domain. / Jelly Rolls - #40 / Tumour necrosis factor-like domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.801 Å
AuthorsElegheert, J. / Clay, J.E. / 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 1.2Dec 18, 2019Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen ...pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details ..._pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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: Cerebellin-1
B: Cerebellin-1
C: Cerebellin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,9816
Polymers59,3173
Non-polymers6643
Water0
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5650 Å2
ΔGint-30 kcal/mol
Surface area17460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.580, 170.450, 116.430
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
SymmetryPoint symmetry: (Schoenflies symbol: C2 (2 fold cyclic))

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Components

#1: Protein Cerebellin-1 / Precerebellin


Mass: 19772.318 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CBLN1 / Plasmid: pHLsec / Cell line (production host): HEK293S / Production host: Homo sapiens (human) / References: UniProt: P23435
#2: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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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: 3.33 Å3/Da / Density % sol: 63.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 15% (v/v) glycerol, 8.5% (v/v) isopropanol, 17% (w/v) polyethylene glycol 4000, 0.085 M Na.HEPES pH 7.5 and 0.02 M sodium bromide

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 5, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.8→85.22 Å / Num. obs: 14603 / % possible obs: 73.4 % / Redundancy: 6.5 % / Biso Wilson estimate: 54.6 Å2 / Rmerge(I) obs: 0.056 / Net I/σ(I): 21.7
Reflection shellResolution: 2.8→3.02 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.425 / Mean I/σ(I) obs: 5.6 / % possible all: 19

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Processing

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

5kc5


Resolution: 2.801→68.77 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.64 / Stereochemistry target values: Maximum Likelihood
RfactorNum. reflection% reflection
Rfree0.2267 708 4.86 %
Rwork0.1883 --
obs0.1901 14561 73.17 %
Solvent computationShrinkage radii: 1 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 59.1 Å2
Refinement stepCycle: LAST / Resolution: 2.801→68.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3314 0 42 0 3356
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033451
X-RAY DIFFRACTIONf_angle_d0.7224666
X-RAY DIFFRACTIONf_dihedral_angle_d13.2021244
X-RAY DIFFRACTIONf_chiral_restr0.031507
X-RAY DIFFRACTIONf_plane_restr0.002600
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8005-3.01670.222480.23871011X-RAY DIFFRACTION27
3.0167-3.32030.27971070.24222075X-RAY DIFFRACTION55
3.3203-3.80080.25391760.2193082X-RAY DIFFRACTION83
3.8008-4.78840.20361850.16313760X-RAY DIFFRACTION99
4.7884-68.79080.21871920.17983925X-RAY DIFFRACTION99
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)
12.8648-0.38740.08272.2085-0.04222.9376-0.1598-0.7242-0.42120.07630.07420.25060.0351-0.43440.0850.2536-0.05570.04160.44910.07360.326670.090134.211516.3107
24.42450.6674-0.23552.53690.56823.1198-0.1842-0.457-0.0292-0.08350.1518-0.0626-0.18880.18640.03430.26070.0545-0.02950.29860.04790.190892.635139.210311.1711
33.5721-1.0460.32162.3326-0.03252.5196-0.04160.43110.095-0.11730.1785-0.18030.0648-0.1133-0.10280.2745-0.02420.00280.292-0.0550.242476.901840.0466-5.2777
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resseq 59:195)
2X-RAY DIFFRACTION2(chain B and resseq 59:202)
3X-RAY DIFFRACTION3(chain C and resseq 59:194)

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