8EDC

Structure of C. elegans UNC-5 IG 1+2 Domains

  • Classification: PROTEIN BINDING
  • 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: 2.89 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.246 
  • R-Value Observed: 0.250 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 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 receptor unc-5210Caenorhabditis elegansMutation(s): 0 
Gene Names: unc-5B0273.4
UniProt
Find proteins for Q26261 (Caenorhabditis elegans)
Explore Q26261 
Go to UniProtKB:  Q26261
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ26261
Glycosylation
Glycosylation Sites: 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)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose
B
3N-Glycosylation
Glycosylation Resources
GlyTouCan:  G21290RB
GlyCosmos:  G21290RB
GlyGen:  G21290RB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.89 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.246 
  • R-Value Observed: 0.250 
  • Space Group: C 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 41.282α = 90
b = 130.216β = 90
c = 97.549γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
PHENIXrefinement
Cootmodel building
PHASERphasing

Structure Validation

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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: 2023-10-25
    Changes: Data collection, Refinement description
  • Version 1.2: 2024-08-14
    Changes: Database references