8SNP | pdb_00008snp

Crystal structure of mouse Netrin-1 in complex with samarium ions

• PDB DOI: https://doi.org/10.2210/pdb8SNP/pdb

• Classification: APOPTOSIS
• Organism(s): Mus musculus
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2023-04-27 Released: 2024-02-07 
• Deposition Author(s): Heide, F., Legare, S., Stetefeld, J.
• Funding Organization(s): Canadian Institutes of Health Research (CIHR)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.40 Å
• R-Value Free: 
  0.268 (Depositor), 0.268 (DCC) 
• R-Value Work: 
  0.250 (Depositor), 0.249 (DCC) 
• R-Value Observed: 
  0.251 (Depositor) 

Starting Model: experimental

Literature

Identifying the molecular basis of Laminin N-terminal domain Ca 2+ binding using a hybrid approach.

Legare, S., Heide, F., Gabir, H., Rafiei, F., Meier, M., Padilla-Meier, G.P., Koch, M., Stetefeld, J.

(2024) Biophys J 123: 2422-2430

• PubMed: 38851889 
• DOI: https://doi.org/10.1016/j.bpj.2024.06.005
• Primary Citation Related Structures: 
  8SNP


• PubMed Abstract: 
  

  Ca ²⁺ is a highly abundant ion involved in numerous biological processes, particularly in multicellular eukaryotic organisms where it exerts many of these functions through interactions with Ca ²⁺ binding proteins. The laminin N-terminal (LN) domain is found in members of the laminin and netrin protein families where it plays a critical role in the function of these proteins. The LN domain of laminins and netrins is a Ca ²⁺ binding domain and in many cases requires Ca ²⁺ to perform its biological function. Here, we conduct a detailed examination of the molecular basis of the LN domain Ca ²⁺ interaction combining structural, computational, bioinformatics, and biophysical techniques. By combining computational and bioinformatic techniques with x-ray crystallography we explore the molecular basis of the LN domain Ca ²⁺ interaction and identify a conserved sequence present in Ca ²⁺ binding LN domains. These findings enable a sequence-based prediction of LN domain Ca ²⁺ binding ability. We use thermal shift assays and isothermal titration calorimetry to explore the biophysical properties of the LN domain Ca ²⁺ interaction. We show that the netrin-1 LN domain exhibits a high affinity and specificity for Ca ²⁺ , which structurally stabilizes the LN domain. This study elucidates the molecular foundation of the LN domain Ca ²⁺ binding interaction and provides a detailed functional characterization of this essential interaction, advancing our understanding of protein-Ca ²⁺ dynamics within the context of the LN domain.

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Organizational Affiliation: 
• Department of Chemistry, University of Manitoba, Winnipeg, Manitoba, Canada. Electronic address: [e-mail].
Department of Chemistry, University of Manitoba, Winnipeg, Manitoba, Canada.
Center for Biochemistry II, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany; Institute for Dental Research and Oral Musculoskeletal Biology, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany; Center for Molecular Medicine Cologne, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany.
Department of Chemistry, University of Manitoba, Winnipeg, Manitoba, Canada. Electronic address: [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: SAXS, gel filtration, assay for oligomerization

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 69.96 kDa 
• Atom Count: 3,238 
• Modeled Residue Count: 409 
• Deposited Residue Count: 604 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Netrin-1	A	604	Mus musculus	Mutation(s): 0  Gene Names: Ntn1
UniProt
Find proteins for O09118 (Mus musculus) Explore O09118  Go to UniProtKB:  O09118
Glycosylation
Glycosylation Sites: 3		Go to GlyGen: O09118-1

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	B [auth D]	3		N-Glycosylation
Glycosylation Resources
GlyTouCan: G21290RB GlyCosmos: G21290RB GlyGen: G21290RB

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	C	2		N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	H [auth A], I [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
SM (Subject of Investigation/LOI)	D [auth A], E [auth A], F [auth A], G [auth A]	SAMARIUM (III) ION Sm DOSGOCSVHPUUIA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.40 Å
• R-Value Free:  0.268 (Depositor), 0.268 (DCC) 
• R-Value Work:  0.250 (Depositor), 0.249 (DCC) 
• R-Value Observed: 0.251 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.5	α = 90
b = 69.5	β = 90
c = 333.641	γ = 120

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-02-07 
Deposition Author(s): Heide, F., Legare, S., Stetefeld, J.

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

Revision History  

• Version 1.0: 2024-02-07
  Type: Initial release
  
• Version 1.1: 2024-10-23
  Changes: Structure summary
• Version 1.2: 2025-03-19
  Changes: Database references