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- PDB-5kc5: Crystal structure of the Cbln1 C1q domain trimer -

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Basic information

Entry
Database: PDB / ID: 5kc5
TitleCrystal structure of the Cbln1 C1q domain trimer
ComponentsCerebellin-1
KeywordsSIGNALING PROTEIN / Cerebellin / C1q / 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 / maintenance of synapse structure / negative regulation of excitatory postsynaptic potential / regulation of postsynaptic density assembly / positive regulation of synapse assembly / heterophilic cell-cell adhesion ...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 / maintenance of synapse structure / negative regulation of excitatory postsynaptic potential / regulation of postsynaptic density assembly / positive regulation of synapse assembly / heterophilic cell-cell adhesion / parallel fiber to Purkinje cell synapse / protein secretion / regulation of presynapse assembly / synaptic cleft / synapse assembly / establishment of localization in cell / synapse organization / nervous system development / : / chemical synaptic transmission / postsynaptic membrane / 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: 2.351 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 1.1Jul 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 1.2Jan 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
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cerebellin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,8642
Polymers16,6431
Non-polymers2211
Water99155
1
A: Cerebellin-1
hetero molecules

A: Cerebellin-1
hetero molecules

A: Cerebellin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,5926
Polymers49,9283
Non-polymers6643
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
Buried area5680 Å2
ΔGint-31 kcal/mol
Surface area17150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.420, 83.420, 50.570
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number168
Space group name H-MP6
SymmetryPoint symmetry: (Schoenflies symbol: C3 (3 fold cyclic))

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Components

#1: Protein Cerebellin-1 / Precerebellin


Mass: 16642.820 Da / Num. of mol.: 1
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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 55 / 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: 3.05 Å3/Da / Density % sol: 59.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M sodium malonate pH 7.0, 20% (w/v) polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 1.073 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 6, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.073 Å / Relative weight: 1
Reflection twinOperator: h,-h-k,-l / Fraction: 0.17
ReflectionResolution: 2.35→50.57 Å / Num. obs: 8497 / % possible obs: 100 % / Redundancy: 8.1 % / Biso Wilson estimate: 40.9 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.126 / Net I/σ(I): 15.2
Reflection shellResolution: 2.35→2.41 Å / Redundancy: 8.1 % / Rmerge(I) obs: 1.263 / Mean I/σ(I) obs: 1.8 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIXdev_1772refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1GR3

1gr3


Resolution: 2.351→50.55 Å / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.81 / Stereochemistry target values: TWIN_LSQ_F
Details: Refined with twin operator h, -h-k, -l to account for higher P622 metric symmetry
RfactorNum. reflection% reflection
Rfree0.197 407 4.79 %
Rwork0.1774 --
obs0.1814 8497 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 45.3 Å2
Refinement stepCycle: LAST / Resolution: 2.351→50.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1081 0 14 55 1150
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021120
X-RAY DIFFRACTIONf_angle_d0.5591513
X-RAY DIFFRACTIONf_dihedral_angle_d11.089405
X-RAY DIFFRACTIONf_chiral_restr0.027165
X-RAY DIFFRACTIONf_plane_restr0.002195
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3519-2.69160.29611440.2532656X-RAY DIFFRACTION95
2.6916-3.38910.23231300.20112672X-RAY DIFFRACTION95
3.3891-21.74770.17041330.15142737X-RAY DIFFRACTION95

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