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- PDB-5h49: Crystal structure of Cbln1 -

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Basic information

Entry
Database: PDB / ID: 5h49
TitleCrystal structure of Cbln1
ComponentsCerebellin-1
KeywordsPROTEIN BINDING / Cbln1 / C1q domain / C1q/TNF superfamily / synaptogenesis
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 / postsynaptic membrane / glutamatergic synapse / 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 speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.8 Å
AuthorsZhong, C. / Shen, J. / Zhang, H. / Ding, J.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China31370726 China
Ministry of Science and Technology of China2013CB910404 China
CitationJournal: Cell Rep / Year: 2017
Title: Cbln1 and Cbln4 Are Structurally Similar but Differ in GluD2 Binding Interactions.
Authors: Chen Zhong / Jinlong Shen / Huibing Zhang / Guangyi Li / Senlin Shen / Fang Wang / Kuan Hu / Longxing Cao / Yongning He / Jianping Ding /
Abstract: Unlike cerebellin 1 (Cbln1), which bridges neurexin (Nrxn) receptors and δ-type glutamate receptors in a trans-synaptic triad, Cbln4 was reported to have no or weak binding for the receptors ...Unlike cerebellin 1 (Cbln1), which bridges neurexin (Nrxn) receptors and δ-type glutamate receptors in a trans-synaptic triad, Cbln4 was reported to have no or weak binding for the receptors despite sharing ∼70% sequence identity with Cbln1. Here, we report crystal structures of the homotrimers of the C1q domain of Cbln1 and Cbln4 at 2.2 and 2.3 Å resolution, respectively. Comparison of the structures suggests that the difference between Cbln1 and Cbln4 in GluD2 binding might be because of their sequence and structural divergence in loop CD. Surprisingly, we show that Cbln4 binds to Nrxn1β and forms a stable complex with the laminin, nectin, sex-hormone binding globulin (LNS) domain of Nrxn1β. Furthermore, the negative-stain electron microscopy reconstruction of hexameric full-length Cbln1 at 13 Å resolution and that of the Cbln4/Nrxn1β complex at 19 Å resolution suggest that Nrxn1β binds to the N-terminal region of Cbln4, probably through strand β10 of the S4 insert.
History
DepositionOct 31, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 13, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Database references / Category: citation / citation_author
Revision 1.2Nov 8, 2017Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.host_org_common_name / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name
Revision 1.3Jan 17, 2018Group: Database references / Category: citation / citation_author
Revision 1.4Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Refinement description / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / refine_hist / 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 / _refine_hist.d_res_low / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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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)61,4784
Polymers61,2573
Non-polymers2211
Water39622
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5250 Å2
ΔGint-34 kcal/mol
Surface area16030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.638, 91.638, 151.046
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Cerebellin-1 / Precerebellin


Mass: 20418.984 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Cbln1 / Production host: Homo sapiens (human) / References: UniProt: P63182
#2: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


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 / Water


Mass: 18.015 Da / Num. of mol.: 22 / Source method: isolated from a natural source / Formula: H2O

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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: 2.59 Å3/Da / Density % sol: 52.48 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 0.1 M Na/K phosphate, pH 6.2, 2.5 M NaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9795 Å
DetectorType: RAYONIX MX-325 / Detector: CCD / Date: Oct 31, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 16418 / % possible obs: 99.8 % / Redundancy: 6.4 % / Net I/σ(I): 15.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
HKL-2000data processing
HKL-2000data scaling
PHENIXphasing
RefinementResolution: 2.8→50 Å / Cor.coef. Fo:Fc: 0.852 / Cor.coef. Fo:Fc free: 0.795 / SU B: 14.477 / SU ML: 0.288 / Cross valid method: THROUGHOUT / ESU R: 0.786 / ESU R Free: 0.393 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.30696 829 5.1 %RANDOM
Rwork0.27142 ---
obs0.27318 15534 99.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.616 Å2
Baniso -1Baniso -2Baniso -3
1--0.37 Å20 Å20 Å2
2---0.37 Å20 Å2
3---0.73 Å2
Refinement stepCycle: 1 / Resolution: 2.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3088 0 14 22 3124
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0193169
X-RAY DIFFRACTIONr_bond_other_d0.0050.023015
X-RAY DIFFRACTIONr_angle_refined_deg1.0041.9374275
X-RAY DIFFRACTIONr_angle_other_deg0.98536887
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.955384
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.94723.356149
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.89615530
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.6081522
X-RAY DIFFRACTIONr_chiral_restr0.0370.2468
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023599
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02805
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.7733.0451554
X-RAY DIFFRACTIONr_mcbond_other3.7733.0461553
X-RAY DIFFRACTIONr_mcangle_it6.4844.5551932
X-RAY DIFFRACTIONr_mcangle_other6.4824.5541933
X-RAY DIFFRACTIONr_scbond_it3.2193.3231615
X-RAY DIFFRACTIONr_scbond_other3.2183.3221616
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.1694.872344
X-RAY DIFFRACTIONr_long_range_B_refined12.51356.1912565
X-RAY DIFFRACTIONr_long_range_B_other12.51256.18712566
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.804→2.877 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.385 57 -
Rwork0.306 1107 -
obs--99.66 %

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