8EDK

Structure of C. elegans UNC-6 LamN and EGF domains

  • Classification: SIGNALING PROTEIN
  • Organism(s): Caenorhabditis elegans
  • Expression System: Trichoplusia ni
  • Mutation(s): No 

  • Deposited: 2022-09-04 Released: 2023-01-11 
  • Deposition Author(s): Priest, J.M., Ozkan, E.
  • Funding Organization(s): National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.222 

Starting Model: in silico
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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Structural insights into the formation of repulsive netrin guidance complexes.

Priest, J.M.Nichols, E.L.Smock, R.G.Hopkins, J.B.Mendoza, J.L.Meijers, R.Shen, K.Ozkan, E.

(2024) Sci Adv 10: eadj8083-eadj8083

  • DOI: https://doi.org/10.1126/sciadv.adj8083
  • Primary Citation of Related Structures:  
    8EDC, 8EDI, 8EDK

  • PubMed Abstract: 

    Netrins dictate attractive and repulsive responses during axon growth and cell migration, where the presence of the receptor Uncoordinated-5 (UNC-5) on target cells results in repulsion. Here, we showed that UNC-5 is a heparin-binding protein, determined its structure bound to a heparin fragment, and could modulate UNC-5-heparin affinity using a directed evolution platform or structure-based rational design. We demonstrated that UNC-5 and UNC-6/netrin form a large, stable, and rigid complex in the presence of heparin, and heparin and UNC-5 exclude the attractive UNC-40/DCC receptor from binding to UNC-6/netrin to a large extent. Caenorhabditis elegans with a heparin-binding-deficient UNC-5 fail to establish proper gonad morphology due to abrogated cell migration, which relies on repulsive UNC-5 signaling in response to UNC-6. Combining UNC-5 mutations targeting heparin and UNC-6/netrin contacts results in complete cell migration and axon guidance defects. Our findings establish repulsive netrin responses to be mediated through a glycosaminoglycan-regulated macromolecular complex.


  • Organizational Affiliation

    Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Netrin unc-6449Caenorhabditis elegansMutation(s): 0 
Gene Names: unc-6unc-106F41C6.1
UniProt
Find proteins for P34710 (Caenorhabditis elegans)
Explore P34710 
Go to UniProtKB:  P34710
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP34710
Glycosylation
Glycosylation Sites: 2
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)][alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose
B
6N/AN-Glycosylation
Glycosylation Resources
GlyTouCan:  G88303DD
GlyCosmos:  G88303DD
GlyGen:  G88303DD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.222 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.243α = 90
b = 70.243β = 90
c = 287.353γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XDSdata scaling
PHASERphasing
PHENIXrefinement
Cootmodel building

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)United StatesR01 NS097161
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesT32 GM138826

Revision History  (Full details and data files)

  • Version 1.0: 2023-01-11
    Type: Initial release
  • Version 1.1: 2024-04-03
    Changes: Data collection, Refinement description
  • Version 1.2: 2024-08-14
    Changes: Database references
  • Version 1.3: 2024-11-13
    Changes: Structure summary