8EDI

Structure of C. elegans UNC-5 IG 1+2 Domains bound to Heparin dp4

• PDB DOI: https://doi.org/10.2210/pdb8EDI/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: 2.11 Å
• R-Value Free: 0.272 
• R-Value Work: 0.240 
• R-Value Observed: 0.242 

Literature

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

Priest, J.M., Ozkan, E.

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.

Macromolecule Content

• Total Structure Weight: 48.67 kDa 
• Atom Count: 3,324 
• Modelled Residue Count: 400 
• Deposited Residue Count: 420 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Netrin receptor unc-5	A, B	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	C, D	3		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G21290RB GlyCosmos:  G21290RB GlyGen:  G21290RB

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
4-deoxy-2-O-sulfo-alpha-L-threo-hex-4-enopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose	E	4		N/A
Glycosylation Resources
GlyTouCan:  G88016IC GlyCosmos:  G88016IC

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.11 Å
• R-Value Free: 0.272 
• R-Value Work: 0.240 
• R-Value Observed: 0.242 
• Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.46	α = 90
b = 69.46	β = 90
c = 424.99	γ = 120

Software Package:

Software Name	Purpose
XDS	data reduction
STARANISO	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: 2023-10-25
  Changes: Data collection, Refinement description