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- PDB-7ol2: Crystal structure of mouse contactin 1 immunoglobulin domains -

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Basic information

Entry
Database: PDB / ID: 7ol2
TitleCrystal structure of mouse contactin 1 immunoglobulin domains
ComponentsContactin-1
KeywordsCELL ADHESION / Zipper / Dimer / Glycoprotein / Immunoglobulin cell adhesion protein Neural cell adhesion protein / Horseshoe
Function / homology
Function and homology information


central nervous system myelin formation / positive regulation of sodium ion transport / side of membrane / Notch signaling pathway / myelination / cerebellum development / locomotory behavior / positive regulation of neuron projection development / neuron projection development / myelin sheath ...central nervous system myelin formation / positive regulation of sodium ion transport / side of membrane / Notch signaling pathway / myelination / cerebellum development / locomotory behavior / positive regulation of neuron projection development / neuron projection development / myelin sheath / presynaptic membrane / carbohydrate binding / gene expression / postsynaptic membrane / cell adhesion / synapse / positive regulation of gene expression / glutamatergic synapse / plasma membrane
Similarity search - Function
Contactin-1 / : / : / : / Immunoglobulin / Immunoglobulin domain / Immunoglobulin domain / Immunoglobulin I-set / Immunoglobulin I-set domain / Fibronectin type III domain ...Contactin-1 / : / : / : / Immunoglobulin / Immunoglobulin domain / 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
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.89 Å
AuthorsChataigner, L.M.P. / Janssen, B.J.C.
Funding support Netherlands, 1items
OrganizationGrant numberCountry
European Research Council (ERC) Netherlands
CitationJournal: Nat Commun / Year: 2022
Title: Structural insights into the contactin 1 - neurofascin 155 adhesion complex.
Authors: Chataigner, L.M.P. / Gogou, C. / den Boer, M.A. / Frias, C.P. / Thies-Weesie, D.M.E. / Granneman, J.C.M. / Heck, A.J.R. / Meijer, D.H. / Janssen, B.J.C.
History
DepositionMay 19, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 14, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Contactin-1
B: Contactin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)139,51314
Polymers133,8152
Non-polymers5,69812
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry, Analytical Centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8520 Å2
ΔGint69 kcal/mol
Surface area65080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.959, 134.162, 181.740
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 37 through 606 or resid 611 through 615 or resid 617 through 618))
21(chain B and (resid 37 through 606 or resid 611 through 615 or resid 617 through 618))

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 37 through 606 or resid 611 through 615 or resid 617 through 618))A37 - 606
121(chain A and (resid 37 through 606 or resid 611 through 615 or resid 617 through 618))A611 - 615
131(chain A and (resid 37 through 606 or resid 611 through 615 or resid 617 through 618))A617 - 618
211(chain B and (resid 37 through 606 or resid 611 through 615 or resid 617 through 618))B37 - 606
221(chain B and (resid 37 through 606 or resid 611 through 615 or resid 617 through 618))B611 - 615
231(chain B and (resid 37 through 606 or resid 611 through 615 or resid 617 through 618))B617 - 618

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Components

#1: Protein Contactin-1 / Neural cell surface protein F3


Mass: 66907.609 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cntn1 / Production host: Homo sapiens (human) / References: UniProt: P12960
#2: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#4: Polysaccharide alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#5: 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.: 5 / Source method: obtained synthetically / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
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
Has ligand of interestY
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: 4.23 Å3/Da / Density % sol: 70.95 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 5.9
Details: 20% w/v PEG 3350 and 0.2 M Magnesium nitrate hexahydrate pH 5.9

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 31, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 3.89→108.09 Å / Num. obs: 20221 / % possible obs: 93.9 % / Redundancy: 9.3 % / CC1/2: 0.961 / Net I/σ(I): 4.4
Reflection shellResolution: 3.89→4.27 Å / Mean I/σ(I) obs: 1.5 / Num. unique obs: 3909 / CC1/2: 0.524

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.27data extraction
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2OM5

2om5


Resolution: 3.89→107.94 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2695 977 4.85 %
Rwork0.2199 19182 -
obs0.2223 20159 93.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 201.77 Å2 / Biso mean: 105.278 Å2 / Biso min: 39.79 Å2
Refinement stepCycle: final / Resolution: 3.89→107.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8996 0 376 0 9372
Biso mean--148.45 --
Num. residues----1136
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A5493X-RAY DIFFRACTION8.474TORSIONAL
12B5493X-RAY DIFFRACTION8.474TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.89-4.10.3276980.27322025212371
4.1-4.360.28161200.23392519263987
4.36-4.690.26881380.2022839297799
4.69-5.160.23371420.192729053047100
5.16-5.910.23311530.198428983051100
5.91-7.450.2791710.238229193090100
7.45-107.940.28471550.22630773232100

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