8AFO

Structure of fibronectin 2 and 3 of L1CAM at 2.0 Angstrom


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.195 

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Literature

X-ray structure and function of fibronectin domains two and three of the neural cell adhesion molecule L1.

Guedez, G.Loers, G.Jeffries, C.M.Kozak, S.Meijers, R.Svergun, D.I.Schachner, M.Low, C.

(2023) FASEB J 37: e22823-e22823

  • DOI: https://doi.org/10.1096/fj.202201511R
  • Primary Citation of Related Structures:  
    8AFO, 8AFP

  • PubMed Abstract: 

    The cell adhesion molecule L1 (L1CAM, L1 in short) plays crucial roles during neural development, regeneration after injury, synapse formation, synaptic plasticity and tumor cell migration. L1 belongs to the immunoglobulin superfamily and comprises in its extracellular part six immunoglobulin (Ig)-like domains and five fibronectin type III homologous repeats (FNs). The second Ig-like domain has been validated for self- (so-called homophilic) binding between cells. Antibodies against this domain inhibit neuronal migration in vitro and in vivo. The fibronectin type III homologous repeats FN2 and FN3 bind small molecule agonistic L1 mimetics and contribute to signal transduction. FN3 has a stretch of 25 amino acids that can be triggered with a monoclonal antibody, or the L1 mimetics, to enhance neurite outgrowth and neuronal cell migration in vitro and in vivo. To correlate the structural features of these FNs with function, we determined a high-resolution crystal structure of a FN2FN3 fragment, which is functionally active in cerebellar granule cells and binds several mimetics. The structure illustrates that both domains are connected by a short linker sequence allowing a flexible and largely independent organization of both domains. This becomes further evident by comparing the X-ray crystal structure with models derived from Small-Angle X-ray Scattering (SAXS) data for FN2FN3 in solution. Based on the X-ray crystal structure, we identified five glycosylation sites which we believe are crucial for folding and stability of these domains. Our study signifies an advance in the understanding of structure-functional relationships of L1.


  • Organizational Affiliation

    Centre for Structural Systems Biology (CSSB), Hamburg, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Neural cell adhesion molecule L1216Homo sapiensMutation(s): 0 
Gene Names: L1CAMCAML1MIC5
UniProt & NIH Common Fund Data Resources
Find proteins for P32004 (Homo sapiens)
Explore P32004 
Go to UniProtKB:  P32004
PHAROS:  P32004
GTEx:  ENSG00000198910 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP32004
Glycosylation
Glycosylation Sites: 5Go to GlyGen: P32004-1
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
B
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.195 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.083α = 90
b = 96.749β = 90
c = 105.853γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2023-03-08
    Type: Initial release