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- PDB-5y4m: Discoidin domain of human CASPR2 -

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Basic information

Entry
Database: PDB / ID: 5y4m
TitleDiscoidin domain of human CASPR2
Componentshuman CASPR2 Disc domain
KeywordsCELL ADHESION / epitope for autoantibody
Function / homology
Function and homology information


limbic system development / clustering of voltage-gated potassium channels / neuron recognition / vocal learning / protein localization to juxtaparanode region of axon / paranodal junction / superior temporal gyrus development / thalamus development / vocalization behavior / paranode region of axon ...limbic system development / clustering of voltage-gated potassium channels / neuron recognition / vocal learning / protein localization to juxtaparanode region of axon / paranodal junction / superior temporal gyrus development / thalamus development / vocalization behavior / paranode region of axon / striatum development / juxtaparanode region of axon / adult behavior / transmission of nerve impulse / social behavior / positive regulation of gap junction assembly / axolemma / prepulse inhibition / voltage-gated potassium channel complex / neuron projection morphogenesis / learning / synaptic membrane / brain development / cerebral cortex development / neuron projection development / perikaryon / protease binding / transmembrane transporter binding / cell population proliferation / early endosome / cell adhesion / axon / neuronal cell body / dendrite / Golgi apparatus / enzyme binding / cell surface / membrane
Similarity search - Function
Neurexin/syndecan/glycophorin C / putative band 4.1 homologues' binding motif / Laminin G domain / Laminin G domain profile. / Laminin G domain / Laminin G domain / Coagulation factors 5/8 type C domain (FA58C) signature 2. / Fibrinogen, alpha/beta/gamma chain, C-terminal globular domain / Fibrinogen-like, C-terminal / Fibrinogen C-terminal domain profile. ...Neurexin/syndecan/glycophorin C / putative band 4.1 homologues' binding motif / Laminin G domain / Laminin G domain profile. / Laminin G domain / Laminin G domain / Coagulation factors 5/8 type C domain (FA58C) signature 2. / Fibrinogen, alpha/beta/gamma chain, C-terminal globular domain / Fibrinogen-like, C-terminal / Fibrinogen C-terminal domain profile. / Coagulation factors 5/8 type C domain (FA58C) signature 1. / Coagulation factor 5/8 C-terminal domain, discoidin domain / Coagulation factors 5/8 type C domain (FA58C) profile. / F5/8 type C domain / Coagulation factor 5/8 C-terminal domain / Galactose-binding domain-like / Epidermal growth factor-like domain. / EGF-like domain profile. / EGF-like domain / Galactose-binding-like domain superfamily / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Contactin-associated protein-like 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.31 Å
AuthorsLiu, H. / Xu, F. / Zhang, J. / Liang, W.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China81322047 China
National Natural Science Foundation of China81673525 China
CitationJournal: J. Autoimmun. / Year: 2019
Title: Structural mapping of hot spots within human CASPR2 discoidin domain for autoantibody recognition.
Authors: Liang, W. / Zhang, J. / Saint-Martin, M. / Xu, F. / Noraz, N. / Liu, J. / Honnorat, J. / Liu, H.
History
DepositionAug 4, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 8, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: human CASPR2 Disc domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,2204
Polymers17,0341
Non-polymers1863
Water3,729207
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area460 Å2
ΔGint8 kcal/mol
Surface area6940 Å2
Unit cell
Length a, b, c (Å)36.250, 59.680, 62.599
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein human CASPR2 Disc domain / Contactin-associated protein-like 2


Mass: 17033.777 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CNTNAP2, CASPR2, KIAA0868 / Production host: Homo sapiens (human) / References: UniProt: Q9UHC6
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 207 / 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: 1.89 Å3/Da / Density % sol: 35 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / pH: 6.2
Details: 20% PEG8000,100 mM Na2HPO4/KH2PO4, pH 6.2, 200 mM NaCl
PH range: 5.8-6.4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.978 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 11, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.31→50 Å / Num. obs: 33381 / % possible obs: 99.6 % / Redundancy: 8.5 % / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.028 / Rrim(I) all: 0.083 / Rsym value: 0.074 / Χ2: 1.387 / Net I/σ(I): 35.36
Reflection shellResolution: 1.31→1.33 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.538 / Mean I/σ(I) obs: 2.75 / Num. unique obs: 1598 / CC1/2: 0.85 / Rpim(I) all: 0.227 / Rrim(I) all: 0.586 / Rsym value: 0.501 / Χ2: 1.005 / % possible all: 97.3

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
HKL-3000data processing
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.31→43.195 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 15.24
RfactorNum. reflection% reflection
Rfree0.1658 1586 4.76 %
Rwork0.1365 --
obs0.1379 33331 99.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.31→43.195 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1181 0 12 207 1400
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051246
X-RAY DIFFRACTIONf_angle_d0.8581695
X-RAY DIFFRACTIONf_dihedral_angle_d24.627454
X-RAY DIFFRACTIONf_chiral_restr0.084167
X-RAY DIFFRACTIONf_plane_restr0.005222
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3087-1.35090.21711350.17242779X-RAY DIFFRACTION98
1.3509-1.39920.20791280.14812878X-RAY DIFFRACTION100
1.3992-1.45520.18471400.13412863X-RAY DIFFRACTION100
1.4552-1.52150.16651670.12632831X-RAY DIFFRACTION100
1.5215-1.60170.16511640.12342821X-RAY DIFFRACTION100
1.6017-1.7020.15211410.1192892X-RAY DIFFRACTION100
1.702-1.83350.1371200.11372893X-RAY DIFFRACTION100
1.8335-2.0180.16761560.12292898X-RAY DIFFRACTION100
2.018-2.310.15121490.12762900X-RAY DIFFRACTION100
2.31-2.91020.19161360.15162945X-RAY DIFFRACTION100
2.9102-43.21870.15941500.14333045X-RAY DIFFRACTION99

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