9D77 | pdb_00009d77

Crystal form of Netrin-1 mimics nanotubes

• PDB DOI: https://doi.org/10.2210/pdb9D77/pdb

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


• Deposited: 2024-08-16 Released: 2024-10-09 
• Deposition Author(s): Meier, M., Krahn, N.J., McDougall, M.D., Rafiei, F., Koch, M., Stetefeld, J.
• Funding Organization(s): Canadian Institutes of Health Research (CIHR), German Research Foundation (DFG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.40 Å
• R-Value Free: 
  0.335 (Depositor), 0.325 (DCC) 
• R-Value Work: 
  0.297 (Depositor), 0.290 (DCC) 

Starting Model: experimental

Literature

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

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 and generated by PISA (software)

Biological Assembly Evidence: SAXS

Macromolecule Content 

• Total Structure Weight: 52.99 kDa 
• Atom Count: 3,578 
• Modeled Residue Count: 417 
• Deposited Residue Count: 443 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Netrin-1	A	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	3D 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	6		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G82348BZ GlyCosmos:  G82348BZ GlyGen:  G82348BZ

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D 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	5		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G22768VO GlyCosmos:  G22768VO GlyGen:  G22768VO

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	E [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
MPD	H [auth A], I [auth A]	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N
CA	F [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL	G [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.40 Å
• R-Value Free:  0.335 (Depositor), 0.325 (DCC) 
• R-Value Work:  0.297 (Depositor), 0.290 (DCC) 

Diffraction Data: https://doi.org/10.18430/M39D77

Space Group: P 6

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 189.26	α = 90
b = 189.26	β = 90
c = 45.88	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-3000	data collection
XDS	data reduction
XSCALE	data scaling
PHASER	phasing
Coot	model building

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-10-09 
Deposition Author(s): Meier, M., Krahn, N.J., McDougall, M.D., Rafiei, F., Koch, M., Stetefeld, J.

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Funding Organization	Location	Grant Number
Canadian Institutes of Health Research (CIHR)	Canada	CIHR-PJT 152935
German Research Foundation (DFG)	Germany	DFG-FOR2722

Revision History  

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