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- PDB-5kwr: Crystal structure of rat Cerebellin-1 -

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Basic information

Entry
Database: PDB / ID: 5kwr
TitleCrystal structure of rat Cerebellin-1
ComponentsCerebellin-1
KeywordsPROTEIN BINDING / Synapse Protein / Extracellular Protein / Glycoprotein / Nervous System
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 / MOLECULAR REPLACEMENT / Resolution: 1.795 Å
AuthorsCheng, S. / Ozkan, E.
Funding support United States, 1items
OrganizationGrant numberCountry
Klingenstein Foundation United States
CitationJournal: Structure / Year: 2016
Title: Conformational Plasticity in the Transsynaptic Neurexin-Cerebellin-Glutamate Receptor Adhesion Complex.
Authors: Cheng, S. / Seven, A.B. / Wang, J. / Skiniotis, G. / Ozkan, E.
History
DepositionJul 18, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 3, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 28, 2016Group: Database references
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_special_symmetry / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_special_symmetry.label_asym_id / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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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)16,7832
Polymers16,2121
Non-polymers5711
Water1,45981
1
A: Cerebellin-1
hetero molecules

A: Cerebellin-1
hetero molecules

A: Cerebellin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,3496
Polymers48,6373
Non-polymers1,7123
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_635-y+1,x-y-2,z1
crystal symmetry operation3_865-x+y+3,-x+1,z1
Buried area7560 Å2
ΔGint-4 kcal/mol
Surface area17520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.740, 82.740, 50.370
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))
Components on special symmetry positions
IDModelComponents
11A-1067-

HOH

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Components

#1: Protein Cerebellin-1 / Precerebellin


Mass: 16212.344 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Cbln1 / Cell line (production host): High Five (BTI-TN-5B1-4) / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P63182
#2: Polysaccharide alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]2-acetamido-2-deoxy-beta- ...alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-3[DGlcpNAcb1-4]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2-1/a3-b1_a4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(3+1)][a-L-Fucp]{}[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 81 / 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: 3.07 Å3/Da / Density % sol: 59.93 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M Tris pH 7.5, 3 M Sodium formate. Grown in the presence of Neurexin-beta

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03321 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 30, 2015
RadiationMonochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03321 Å / Relative weight: 1
ReflectionResolution: 1.795→50 Å / Num. obs: 18152 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Redundancy: 6.46 % / Biso Wilson estimate: 39.49 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.04 / Rsym value: 0.04 / Net I/σ(I): 22.5
Reflection shellResolution: 1.8→1.84 Å / Redundancy: 3.15 % / Rmerge(I) obs: 0.644 / Mean I/σ(I) obs: 1.74 / CC1/2: 0.729 / % possible all: 83.8

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Processing

Software
NameVersionClassification
PHENIX(dev_2471: ???)refinement
XDSVersion Oct 15, 2015data reduction
XDSVersion Oct 15, 2015data scaling
PHASER2.6.0phasing
Coot0.8.3model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4OUM

4oum


Resolution: 1.795→41.37 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.3 / Details: TLS refinement
RfactorNum. reflection% reflection
Rfree0.1888 1774 9.78 %
Rwork0.1601 --
obs0.1629 18144 98.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.795→41.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1103 0 38 81 1222
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051188
X-RAY DIFFRACTIONf_angle_d0.741612
X-RAY DIFFRACTIONf_dihedral_angle_d9.106696
X-RAY DIFFRACTIONf_chiral_restr0.057180
X-RAY DIFFRACTIONf_plane_restr0.004205
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7955-1.8440.33431120.33151050X-RAY DIFFRACTION84
1.844-1.89830.27381370.26171212X-RAY DIFFRACTION95
1.8983-1.95960.23091350.19181218X-RAY DIFFRACTION97
1.9596-2.02960.19541380.16331285X-RAY DIFFRACTION100
2.0296-2.11090.20451400.15481276X-RAY DIFFRACTION100
2.1109-2.20690.19871310.16741294X-RAY DIFFRACTION100
2.2069-2.32330.19441420.16221250X-RAY DIFFRACTION100
2.3233-2.46880.17691440.16071285X-RAY DIFFRACTION100
2.4688-2.65940.23281360.17731298X-RAY DIFFRACTION100
2.6594-2.9270.22121340.16941285X-RAY DIFFRACTION100
2.927-3.35030.18531430.1521290X-RAY DIFFRACTION100
3.3503-4.22040.16461400.13431295X-RAY DIFFRACTION100
4.2204-41.3810.16881420.15781332X-RAY DIFFRACTION100
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)
16.517-1.824-1.52639.85076.29834.16430.16550.59190.0365-1.2492-0.07220.1936-1.46640.1927-0.06630.2622-0.0267-0.06040.3060.01550.3126113.9444-21.256-27.2764
25.58144.6081-0.35536.9208-0.46884.42620.1572-0.32990.42680.6245-0.13470.8288-0.1412-0.6007-0.02560.23050.02350.03840.3488-0.03080.3472102.4179-22.5429-7.3266
31.9705-0.1482-0.69181.93261.83946.4193-0.02420.3317-0.0331-0.1858-0.00020.1913-0.2214-0.48350.02260.1994-0.0317-0.01620.30940.01860.2853110.8462-24.6044-20.7717
43.66280.0883-0.31797.89871.59863.8081-0.124-0.5224-0.00060.72670.15460.12320.08930.05070.02980.2017-0.00580.03360.3450.03680.2531113.5934-28.5757-3.0594
52.6852-0.7034-0.93313.91831.46724.7537-0.1321-0.0861-0.10960.17160.10220.25220.316-0.09240.07320.1656-0.02930.00260.24990.03510.2517111.7132-28.2525-11.8013
68.217-1.2378-2.94323.227-1.85354.50340.08320.7669-0.3813-0.6127-0.14170.12930.2057-0.13940.11960.1692-0.032-0.03970.2066-0.00550.2143117.7841-29.2484-27.5856
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 57 through 67 )
2X-RAY DIFFRACTION2chain 'A' and (resid 68 through 87 )
3X-RAY DIFFRACTION3chain 'A' and (resid 88 through 120 )
4X-RAY DIFFRACTION4chain 'A' and (resid 121 through 150 )
5X-RAY DIFFRACTION5chain 'A' and (resid 151 through 183 )
6X-RAY DIFFRACTION6chain 'A' and (resid 184 through 195 )

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