7OL2 | pdb_00007ol2

Crystal structure of mouse contactin 1 immunoglobulin domains


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.89 Å
  • R-Value Free: 
    0.270 (Depositor), 0.267 (DCC) 
  • R-Value Work: 
    0.220 (Depositor), 0.222 (DCC) 
  • R-Value Observed: 
    0.222 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Structural insights into the contactin 1 - neurofascin 155 adhesion complex.

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.

(2022) Nat Commun 13: 6607-6607

  • DOI: https://doi.org/10.1038/s41467-022-34302-9
  • Primary Citation Related Structures: 
    7OK5, 7OL2, 7OL4

  • PubMed Abstract: 

    Cell-surface expressed contactin 1 and neurofascin 155 control wiring of the nervous system and interact across cells to form and maintain paranodal myelin-axon junctions. The molecular mechanism of contactin 1 - neurofascin 155 adhesion complex formation is unresolved. Crystallographic structures of complexed and individual contactin 1 and neurofascin 155 binding regions presented here, provide a rich picture of how competing and complementary interfaces, post-translational glycosylation, splice differences and structural plasticity enable formation of diverse adhesion sites. Structural, biophysical, and cell-clustering analysis reveal how conserved Ig1-2 interfaces form competing heterophilic contactin 1 - neurofascin 155 and homophilic neurofascin 155 complexes whereas contactin 1 forms low-affinity clusters through interfaces on Ig3-6. The structures explain how the heterophilic Ig1-Ig4 horseshoe's in the contactin 1 - neurofascin 155 complex define the 7.4 nm paranodal spacing and how the remaining six domains enable bridging of distinct intercellular distances.


  • Organizational Affiliation
    • Structural Biochemistry, Bijvoet Center for Biomolecular Research, Faculty of Science, Utrecht University, Universiteitsweg 99, 3584 CG, Utrecht, The Netherlands.

Macromolecule Content 

  • Total Structure Weight: 139.51 kDa 
  • Atom Count: 9,372 
  • Modeled Residue Count: 1,136 
  • Deposited Residue Count: 1,184 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Contactin-1
A, B
592Mus musculusMutation(s): 0 
Gene Names: Cntn1
UniProt
Find proteins for P12960 (Mus musculus)
Explore P12960 
Go to UniProtKB:  P12960
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP12960
Glycosylation
Glycosylation Sites: 6Go to GlyGen: P12960-1
Sequence Annotations
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Reference Sequence

Oligosaccharides

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Entity ID: 2
MoleculeChains Length2D Diagram GlycosylationD Interactions
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
C, D
5N-Glycosylation
Glycosylation Resources
GlyTouCan: G22768VO
GlyCosmos: G22768VO
GlyGen: G22768VO
Entity ID: 3
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
E, G, I
2N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT
GlyCosmos: G42666HT
GlyGen: G42666HT
Entity ID: 4
MoleculeChains Length2D Diagram GlycosylationD Interactions
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
F, H
4N-Glycosylation
Glycosylation Resources
GlyTouCan: G81315DD
GlyCosmos: G81315DD
GlyGen: G81315DD

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.89 Å
  • R-Value Free:  0.270 (Depositor), 0.267 (DCC) 
  • R-Value Work:  0.220 (Depositor), 0.222 (DCC) 
  • R-Value Observed: 0.222 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 92.959α = 90
b = 134.162β = 90
c = 181.74γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
xia2data reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research Council (ERC)Netherlands--

Revision History  (Full details and data files)

  • Version 1.0: 2022-12-14
    Type: Initial release
  • Version 1.1: 2024-01-31
    Changes: Data collection, Refinement description
  • Version 1.2: 2024-11-13
    Changes: Structure summary