7LRF | pdb_00007lrf

Netrin-1 in complex with SOS

• PDB DOI: https://doi.org/10.2210/pdb7LRF/pdb

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


• Deposited: 2021-02-16 Released: 2022-02-23 
• Deposition Author(s): Gupta, M., McDougall, M., Torres, A.M., Stetefeld, J.
• Funding Organization(s): Canadian Institutes of Health Research (CIHR)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.21 Å
• R-Value Free: 
  0.281 (Depositor), 0.279 (DCC) 
• R-Value Work: 
  0.226 (Depositor), 0.226 (DCC) 
• R-Value Observed: 
  0.229 (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.

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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: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 105.49 kDa 
• Atom Count: 6,726 
• Modeled Residue Count: 829 
• Deposited Residue Count: 886 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Netrin-1	A, B	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
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C	3		N-Glycosylation
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

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	D, E, F, G, H, I, J	2		N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
1,3,4,6-tetra-O-sulfo-beta-D-fructofuranose-(2-1)-2,3,4,6-tetra-O-sulfonato-alpha-D-glucopyranose	K, L	2		N/A
Glycosylation Resources
GlyTouCan: G97555GV GlyCosmos: G97555GV

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NHE	T [auth B]	2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID C8 H17 N O3 S MKWKNSIESPFAQN-UHFFFAOYSA-N
PEG	P [auth A], U [auth B]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
EDO	M [auth A], N [auth A], O [auth A], S [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CA	Q [auth A], V [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL	W [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	R [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Biologically Interesting Molecules (External Reference) 

1 Unique

Entity ID: 4
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900013	K, L	sucrose octasulfate	Oligosaccharide / Substrate analog

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.21 Å
• R-Value Free:  0.281 (Depositor), 0.279 (DCC) 
• R-Value Work:  0.226 (Depositor), 0.226 (DCC) 
• R-Value Observed: 0.229 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.105	α = 90
b = 80.152	β = 90
c = 241.702	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

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

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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: 2023-10-25
  Changes: Data collection, Refinement description
• Version 1.3: 2024-10-16
  Changes: Structure summary