8EDC

Structure of C. elegans UNC-5 IG 1+2 Domains

• PDB DOI: https://doi.org/10.2210/pdb8EDC/pdb

• Classification: PROTEIN BINDING
• 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: 2.89 Å
• R-Value Free: 0.285 
• R-Value Work: 0.246 
• R-Value Observed: 0.250 

Literature

Structure of C. elegans UNC-5 IG 1+2 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: 23.95 kDa 
• Atom Count: 1,559 
• Modelled Residue Count: 198 
• Deposited Residue Count: 210 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Netrin receptor unc-5	A	210	Caenorhabditis elegans	Mutation(s): 0  Gene Names: unc-5, B0273.4
UniProt
Find proteins for Q26261 (Caenorhabditis elegans) Explore Q26261  Go to UniProtKB:  Q26261

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	3		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G21290RB GlyCosmos:  G21290RB GlyGen:  G21290RB

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A], D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.89 Å
• R-Value Free: 0.285 
• R-Value Work: 0.246 
• R-Value Observed: 0.250 
• Space Group: C 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.282	α = 90
b = 130.216	β = 90
c = 97.549	γ = 90

Software Package:

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

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: 2023-10-25
  Changes: Data collection, Refinement description