7LER | pdb_00007ler

Netrin-1 filament assembly

• PDB DOI: https://doi.org/10.2210/pdb7LER/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Gallus gallus
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2021-01-14 Released: 2022-02-23 
• Deposition Author(s): McDougall, M., Gupta, M., Stetefeld, J.
• Funding Organization(s): Canadian Institutes of Health Research (CIHR)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 5.99 Å
• R-Value Free: 
  0.368 (Depositor), 0.329 (DCC) 
• R-Value Work: 
  0.304 (Depositor), 0.275 (DCC) 
• R-Value Observed: 
  0.384 (Depositor) 

Starting Model: experimental

Literature

The dynamic nature of netrin-1 and the structural basis for glycosaminoglycan fragment-induced filament formation.

Meier, M., Gupta, M., Akgul, S., McDougall, M., Imhof, T., Nikodemus, D., Reuten, R., Moya-Torres, A., To, V., Ferens, F., Heide, F., Padilla-Meier, G.P., Kukura, P., Huang, W., Gerisch, B., Morgelin, M., Poole, K., Antebi, A., Koch, M., Stetefeld, J.

(2023) Nat Commun 14: 1226-1226

• PubMed: 36869049 
• DOI: https://doi.org/10.1038/s41467-023-36692-w
• Primary Citation Related Structures: 
  7LER, 7LRF


• PubMed Abstract: 
  

  Netrin-1 is a bifunctional chemotropic guidance cue that plays key roles in diverse cellular processes including axon pathfinding, cell migration, adhesion, differentiation, and survival. Here, we present a molecular understanding of netrin-1 mediated interactions with glycosaminoglycan chains of diverse heparan sulfate proteoglycans (HSPGs) and short heparin oligosaccharides. Whereas interactions with HSPGs act as platform to co-localise netrin-1 close to the cell surface, heparin oligosaccharides have a significant impact on the highly dynamic behaviour of netrin-1. Remarkably, the monomer-dimer equilibrium of netrin-1 in solution is abolished in the presence of heparin oligosaccharides and replaced with highly hierarchical and distinct super assemblies leading to unique, yet unknown netrin-1 filament formation. In our integrated approach we provide a molecular mechanism for the filament assembly which opens fresh paths towards a molecular understanding of netrin-1 functions.

---

Organizational Affiliation: 
• Department of Chemistry, University of Manitoba, Winnipeg, Canada.
Center for Biochemistry II, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931, Cologne, Germany.
Max Planck Institute for Biology of Ageing, Cologne, Germany.
Faculty of Biology, Institute of Biology II, Albert Ludwigs University of Freiburg, Freiburg, Germany.
Institute of Experimental and Clinical Pharmacology and Toxicology, Medical Faculty, University of Freiburg, Freiburg, Germany.
Department of Obsterics and Gynecology, Medical Center, University of Freiburg, Freiburg, Germany.
Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford, OX1 3QZ, UK.
Colzyx AB, Lund, Sweden.
Max Delbrück Center for Molecular Medicine, Robert Roessle Str 10, Berlin-Buch, Germany.
EMBL Australia Node in Single Molecule Science, School of Medical Sciences, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia.
Max Planck Institute for Biology of Ageing, Cologne, Germany. [e-mail].
Cologne Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases, University of Cologne, Cologne, 50931, Germany. [e-mail].
Center for Biochemistry II, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931, Cologne, Germany. [e-mail].
Institute for Dental Research and Oral Musculoskeletal Biology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931, Cologne, Germany. [e-mail].
Center for Molecular Medicine Cologne, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931, Cologne, Germany. [e-mail].
Department of Chemistry, University of Manitoba, Winnipeg, Canada. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 48-mer - A48 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 4-mer - A4 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 4-mer - A4 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 4-mer - A4 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 4-mer - A4 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: scanning transmission electron microscopy

Macromolecule Content 

• Total Structure Weight: 410.86 kDa 
• Atom Count: 26,405 
• Modeled Residue Count: 3,249 
• Deposited Residue Count: 3,544 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Netrin-1	A, B, C, D [auth E], E [auth D], F, G, H	443	Gallus gallus	Mutation(s): 0  Gene Names: NTN1
UniProt
Find proteins for Q90922 (Gallus gallus) Explore Q90922  Go to UniProtKB:  Q90922
Glycosylation
Glycosylation Sites: 4

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D 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	I, K, M, O, Q, S, U, W	5		N-Glycosylation
Glycosylation Resources
GlyTouCan: G22768VO GlyCosmos: G22768VO GlyGen: G22768VO

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	J, L, N, P, R, T, V, X	2		N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	AA [auth B], BA [auth B], CA [auth C], DA [auth C], EA [auth E], FA [auth E], GA [auth D], HA [auth D], IA [auth F], JA [auth F], KA [auth G], LA [auth G], MA [auth H], NA [auth H], Y [auth A], Z [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 5.99 Å
• R-Value Free:  0.368 (Depositor), 0.329 (DCC) 
• R-Value Work:  0.304 (Depositor), 0.275 (DCC) 
• R-Value Observed: 0.384 (Depositor) 

Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 196.69	α = 90
b = 196.69	β = 90
c = 476.33	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XSCALE	data scaling
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-02-23 
Deposition Author(s): McDougall, M., Gupta, M., Stetefeld, J.

---

Funding Organization	Location	Grant Number
Canadian Institutes of Health Research (CIHR)	Canada	RPA-109759

Revision History  

• Version 1.0: 2022-02-23
  Type: Initial release
  
• Version 1.1: 2023-03-15
  Changes: Database references
• Version 1.2: 2023-08-16
  Changes: Data collection, Other
• Version 1.3: 2023-10-25
  Changes: Refinement description
• Version 1.4: 2024-11-20
  Changes: Structure summary