8SNP

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 
• R-Value Work: 0.250 
• R-Value Observed: 0.251 

Starting Model: experimental

Literature

Investigating the structural and functional roles of calcium binding in Netrin-1

Legare, S., Heide, F., Gabir, H., Rafiei, F., Meier, M., Koch, M., Stetefeld, J.

To be published.

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 
• Modelled 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	3D 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	3D 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 
• R-Value Work: 0.250 
• R-Value Observed: 0.251 
• 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