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- PDB-5e7l: Crystal structure of mouse CNTN2 FN1-FN3 domains -

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Basic information

Entry
Database: PDB / ID: 5e7l
TitleCrystal structure of mouse CNTN2 FN1-FN3 domains
ComponentsContactin-2
KeywordsCELL ADHESION / Neural cell adhesion molecule / Fibronectin type III domains
Function / homology
Function and homology information


establishment of protein localization to juxtaparanode region of axon / presynaptic membrane organization / positive regulation of adenosine receptor signaling pathway / reduction of food intake in response to dietary excess / regulation of astrocyte differentiation / cell adhesion mediator activity / regulation of axon diameter / clustering of voltage-gated potassium channels / cerebral cortex GABAergic interneuron migration / protein localization to juxtaparanode region of axon ...establishment of protein localization to juxtaparanode region of axon / presynaptic membrane organization / positive regulation of adenosine receptor signaling pathway / reduction of food intake in response to dietary excess / regulation of astrocyte differentiation / cell adhesion mediator activity / regulation of axon diameter / clustering of voltage-gated potassium channels / cerebral cortex GABAergic interneuron migration / protein localization to juxtaparanode region of axon / central nervous system myelination / positive regulation of protein processing / G protein-coupled adenosine receptor signaling pathway / axon initial segment / juxtaparanode region of axon / node of Ranvier / regulation of cell morphogenesis / axonal fasciculation / adult walking behavior / fat cell differentiation / response to dietary excess / regulation of neuronal synaptic plasticity / negative regulation of neuron differentiation / side of membrane / axon guidance / learning / establishment of localization in cell / protein processing / receptor internalization / microtubule cytoskeleton organization / neuron differentiation / neuron migration / neuron projection development / myelin sheath / carbohydrate binding / postsynaptic membrane / neuron projection / axon / neuronal cell body / cell surface
Similarity search - Function
: / Immunoglobulin domain / Immunoglobulin I-set / Immunoglobulin I-set domain / Fibronectin type III domain / Fibronectin type 3 domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Fibronectin type-III domain profile. / Fibronectin type III ...: / Immunoglobulin domain / Immunoglobulin I-set / Immunoglobulin I-set domain / Fibronectin type III domain / Fibronectin type 3 domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.002 Å
AuthorsNikolaienko, R.M. / Bouyain, S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM088806 United States
CitationJournal: J.Biol.Chem. / Year: 2016
Title: Structural Basis for Interactions Between Contactin Family Members and Protein-tyrosine Phosphatase Receptor Type G in Neural Tissues.
Authors: Nikolaienko, R.M. / Hammel, M. / Dubreuil, V. / Zalmai, R. / Hall, D.R. / Mehzabeen, N. / Karuppan, S.J. / Harroch, S. / Stella, S.L. / Bouyain, S.
History
DepositionOct 12, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 31, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 23, 2016Group: Database references
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Database references / Category: citation / pdbx_audit_support
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Contactin-2


Theoretical massNumber of molelcules
Total (without water)32,9911
Polymers32,9911
Non-polymers00
Water3,423190
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)124.390, 40.674, 82.599
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-1005-

HOH

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Components

#1: Protein Contactin-2 / Axonal glycoprotein TAG-1 / Axonin-1 / Transient axonal glycoprotein 1 / TAX-1


Mass: 32990.641 Da / Num. of mol.: 1 / Fragment: FN domains 1-3, UNP residues 609-911
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cntn2, Tax / Plasmid: pT7HMP / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: Q61330
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 190 / 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: 3.17 Å3/Da / Density % sol: 61.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 50 mM NH4Cl, 50 mM Tris-HCl pH 8.5, 10% (w/v) PEG 4000, 2% (v/v) glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 24, 2011
RadiationMonochromator: ROSENBAUM-ROCK DOUBLE-CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionRedundancy: 7 % / Number: 281502 / Rmerge(I) obs: 0.082 / Χ2: 0.94 / D res high: 1.8 Å / D res low: 50 Å / Num. obs: 40036 / % possible obs: 99.1
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)IDRmerge(I) obsChi squaredRedundancy
3.885010.0490.9747
3.083.8810.0850.9317.3
2.693.0810.0880.9197.4
2.442.6910.1051.0127.4
2.272.4410.1340.9967.3
2.132.2710.1611.0067.3
2.032.1310.210.9577.3
1.942.0310.290.9067.1
1.861.9410.3740.8516.6
1.81.8610.4790.8165.6
ReflectionResolution: 2→30 Å / Num. obs: 28357 / % possible obs: 97.8 % / Redundancy: 5.9 % / Biso Wilson estimate: 32.14 Å2 / Rmerge(I) obs: 0.11 / Χ2: 1 / Net I/av σ(I): 12.463 / Net I/σ(I): 10.8 / Num. measured all: 166345
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2-2.073.20.50825201.01189.3
2.07-2.1540.42527140.98395
2.15-2.254.70.38827861.03897.4
2.25-2.375.40.35928381.02299.3
2.37-2.526.20.33228341.05499.1
2.52-2.716.80.26428581.04498.8
2.71-2.997.10.18628540.97399.6
2.99-3.427.10.12629080.9699.6
3.42-4.3170.08729370.99299.8
4.31-306.60.0631080.95699.6

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassification
PHENIXrefinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
PDB_EXTRACT3.15data extraction
Coot0.8.1model building
RefinementMethod to determine structure: SAD / Resolution: 2.002→29.103 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2264 1413 5 %
Rwork0.1908 26868 -
obs0.1926 28281 97.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 131.15 Å2 / Biso mean: 39.2301 Å2 / Biso min: 16.82 Å2
Refinement stepCycle: final / Resolution: 2.002→29.103 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2301 0 0 190 2491
Biso mean---40.5 -
Num. residues----302
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072362
X-RAY DIFFRACTIONf_angle_d1.0593216
X-RAY DIFFRACTIONf_chiral_restr0.045338
X-RAY DIFFRACTIONf_plane_restr0.005425
X-RAY DIFFRACTIONf_dihedral_angle_d12.022869
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0021-2.07370.29741200.27762320244085
2.0737-2.15670.31221350.24572566270195
2.1567-2.25480.27461390.22672643278298
2.2548-2.37360.24631430.22032705284899
2.3736-2.52230.25411420.21552688283099
2.5223-2.71690.2771430.21572716285998
2.7169-2.990.27291420.222527222864100
2.99-3.42210.25071460.19227692915100
3.4221-4.30930.18361470.169427922939100
4.3093-29.10630.17971560.152929473103100

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