8EDK

Structure of C. elegans UNC-6 LamN and EGF domains

• PDB DOI: https://doi.org/10.2210/pdb8EDK/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Caenorhabditis elegans
• Expression System: Trichoplusia ni
• Mutation(s): No 


• Deposited: 2022-09-04 Released: 2023-01-11 
• Deposition Author(s): Priest, J.M., Ozkan, E.
• Funding Organization(s): National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.259 
• R-Value Work: 0.220 
• R-Value Observed: 0.222 

Literature

Structure of C. elegans UNC-6/Netrin LamN and 3 EGF Domains

Priest, J.M., Ozkan, E.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 51.26 kDa 
• Atom Count: 3,314 
• Modelled Residue Count: 412 
• Deposited Residue Count: 449 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Netrin unc-6	A	449	Caenorhabditis elegans	Mutation(s): 0  Gene Names: unc-6, unc-106, F41C6.1
UniProt
Find proteins for P34710 (Caenorhabditis elegans) Explore P34710  Go to UniProtKB:  P34710

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)][alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	B	6	N/A	N-Glycosylation
Glycosylation Resources
GlyTouCan:  G88303DD GlyCosmos:  G88303DD GlyGen:  G88303DD

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	F [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
SO4 (Subject of Investigation/LOI)	C [auth A], D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
CA	E [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.259 
• R-Value Work: 0.220 
• R-Value Observed: 0.222 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.243	α = 90
b = 70.243	β = 90
c = 287.353	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
XDS	data scaling
PHASER	phasing
PHENIX	refinement
Coot	model building

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-01-11 
Deposition Author(s): Priest, J.M., Ozkan, E.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)	United States	R01 NS097161
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	T32 GM138826

Revision History  

• Version 1.0: 2023-01-11
  Type: Initial release
  
• Version 1.1: 2024-04-03
  Changes: Data collection, Refinement description