9D77

Crystal form of Netrin-1 mimics nanotubes


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.40 Å
  • R-Value Free: 0.335 
  • R-Value Work: 0.297 

Starting Model: experimental
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This is version 1.0 of the entry. See complete history


Literature

Mechanistic insights in the higher-order protein assemblies of netrin-1

Rafiei, F.Meier, M.Koch, M.Stetefeld, J.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Netrin-1443Gallus gallusMutation(s): 0 
Gene Names: NTN1
UniProt
Find proteins for Q90922 (Gallus gallus)
Explore Q90922 
Go to UniProtKB:  Q90922
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ90922
Glycosylation
Glycosylation Sites: 4
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

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Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D 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)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose
B
6N-Glycosylation
Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D 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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.40 Å
  • R-Value Free: 0.335 
  • R-Value Work: 0.297 
  • Space Group: P 6
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 189.26α = 90
b = 189.26β = 90
c = 45.88γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
HKL-3000data collection
XDSdata reduction
XSCALEdata scaling
PHASERphasing
Cootmodel building

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Canadian Institutes of Health Research (CIHR)CanadaCIHR-PJT 152935
German Research Foundation (DFG)GermanyDFG-FOR2722

Revision History  (Full details and data files)

  • Version 1.0: 2024-10-09
    Type: Initial release