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- PDB-5kc7: Crystal structure of Cbln1 (Val55-Gly58 deletion mutant) -

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Basic information

Entry
Database: PDB / ID: 5kc7
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. / Tumour necrosis factor-like domain superfamily
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 7.035 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 1.1Feb 20, 2019Group: Advisory / Data collection / Derived calculations
Category: diffrn_source / pdbx_data_processing_status ...diffrn_source / pdbx_data_processing_status / pdbx_validate_symm_contact / struct_conn / struct_conn_type
Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.2Jul 10, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Dec 11, 2019Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_oper_list
Revision 1.4Feb 7, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.pdb_format_compatible

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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
D: Cerebellin-1


Theoretical massNumber of molelcules
Total (without water)79,0894
Polymers79,0894
Non-polymers00
Water0
1
A: Cerebellin-1
B: Cerebellin-1
C: Cerebellin-1
D: Cerebellin-1

D: Cerebellin-1

D: Cerebellin-1


  • defined by author
  • 119 kDa, 6 polymers
Theoretical massNumber of molelcules
Total (without water)118,6346
Polymers118,6346
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_445z-1/2,-x-1/2,-y1
crystal symmetry operation12_455-y-1/2,-z,x+1/21
Unit cell
Length a, b, c (Å)187.450, 187.450, 187.450
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number199
Space group name H-MI213
SymmetryPoint symmetry: (Schoenflies symbol: C2 (2 fold cyclic))
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111(chain A and (resseq 59:69 or (resid 70 and (name...
211(chain B and (resseq 59:172 or (resid 173 and (name...
311(chain C and (resseq 59:69 or (resid 70 and (name...
411(chain D and (resseq 59:69 or (resid 70 and (name...

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Components

#1: Protein
Cerebellin-1 / Precerebellin


Mass: 19772.318 Da / Num. of mol.: 4 / Mutation: (Val55-Gly58 deletion mutant)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CBLN1 / Cell line (production host): HEK293S / Production host: Homo sapiens (human) / References: UniProt: P23435

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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: 3.47 Å3/Da / Density % sol: 64.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 2.75 M 1,6-Hexanediol, 50 mM Tris pH 8.0 and 5 mM magnesium sulphate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 24, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 7→76.55 Å / Num. obs: 1801 / % possible obs: 99.9 % / Redundancy: 9.4 % / CC1/2: 0.998 / Rmerge(I) obs: 0.048 / Net I/σ(I): 28.2
Reflection shellResolution: 7→7.22 Å / Redundancy: 9.9 % / Rmerge(I) obs: 0.394 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(dev_2283: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5KC5

5kc5


Resolution: 7.035→50.098 Å / SU ML: 1.14 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 24.86
RfactorNum. reflection% reflection
Rfree0.351 172 9.59 %
Rwork0.2697 --
obs0.2772 1794 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 7.035→50.098 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4276 0 0 0 4276
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044371
X-RAY DIFFRACTIONf_angle_d0.9165902
X-RAY DIFFRACTIONf_dihedral_angle_d14.9021578
X-RAY DIFFRACTIONf_chiral_restr0.043639
X-RAY DIFFRACTIONf_plane_restr0.002761
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1057X-RAY DIFFRACTIONPOSITIONAL
12B1057X-RAY DIFFRACTIONPOSITIONAL0.002
13C1057X-RAY DIFFRACTIONPOSITIONAL0.001
14D1057X-RAY DIFFRACTIONPOSITIONAL0.001
LS refinement shellResolution: 7.0349→50.0994 Å
RfactorNum. reflection% reflection
Rfree0.351 172 -
Rwork0.2697 1622 -
obs--100 %
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)
19.97445.793-1.59745.0818-0.91126.32653.85641.64713.0435-1.7923-1.5282-1.1445-1.62312.75330.10154.19020.9486-0.1122.71051.0293.434-22.3395-21.110636.2404
22.40242.23382.21784.6957-2.84385.8592-3.2147-1.6223-1.780.78181.3853-3.921-1.4735-0.8488-0.24225.1413-1.03030.55453.80940.37684.3082-15.8085-41.90227.9887
32.1563-0.41238.20910.3032-0.10714.7915-5.48971.85067.23813.71560.73820.68432.0866-0.7719-15.21817.15730.71280.99284.09441.30844.33730.2332-26.337934.0637
44.9299-1.71071.83638.8001-1.59890.70072.7881-1.33972.29163.23920.1908-6.99222.02780.45650.92764.9264-0.3954-0.95673.7230.10492.3817-46.0048-44.450430.151
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain aA59 - 193
2X-RAY DIFFRACTION2chain bB59 - 193
3X-RAY DIFFRACTION3chain cC59 - 193
4X-RAY DIFFRACTION4chain dD59 - 193

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