Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 15.39 kDa 
• Atom Count: 1083 
• Modelled Residue Count: 122 
• Deposited Residue Count: 135 
• Unique protein chains: 1

4D0E

Human Notch1 EGF domains 11-13 mutant GlcNAc-fucose disaccharide modified at T466

• DOI: 10.2210/pdb4D0E/pdb

• Classification: TRANSCRIPTION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2014-04-25 Released: 2014-05-21 
• Deposition Author(s): Taylor, P., Takeuchi, H., Sheppard, D., Chillakuri, C., Lea, S.M., Haltiwanger, R.S., Handford, P.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.61 Å
• R-Value Free: 0.270 
• R-Value Work: 0.231 
• R-Value Observed: 0.232 

Literature

Fringe-Mediated Extension of O-Linked Fucose in the Ligand-Binding Region of Notch1 Increases Binding to Mammalian Notch Ligands.

Taylor, P., Takeuchi, H., Sheppard, D., Chillakuri, C., Lea, S.M., Haltiwanger, R.S., Handford, P.A.

(2014) Proc Natl Acad Sci U S A 111: 7290

• PubMed: 24803430 
• DOI: 10.1073/pnas.1319683111
• Primary Citation of Related Structures:  
  4D0E, 4D0F, 4CUD, 4CUE, 4CUF


• PubMed Abstract: 
  

The Notch signaling pathway is essential for many aspects of development, cell fate determination, and tissue homeostasis. Notch signaling can be modulated by posttranslational modifications to the Notch receptor, which are known to alter both ligand binding and receptor activation. We have modified the ligand-binding region (EGF domains 11-13) of human Notch1 (hN1) with O-fucose and O-glucose glycans and shown by flow cytometry and surface plasmon resonance that the Fringe-catalyzed addition of GlcNAc to the O-fucose at T466 in EGF12 substantially increases binding to Jagged1 and Delta-like 1 (DLL1) ligands. We have subsequently determined the crystal structures of EGF domains 11-13 of hN1 modified with either the O-fucose monosaccharide or the GlcNAc-fucose disaccharide at T466 of EGF12 and observed no change in backbone structure for each variant. Collectively, these data demonstrate a role for GlcNAc in modulating the ligand-binding site in hN1 EGF12, resulting in an increased affinity of this region for ligands Jagged1 and DLL1. We propose that this finding explains the Fringe-catalyzed enhancement of Notch-Delta signaling observed in flies and humans, but suggest that the inhibitory effect of Fringe on Jagged/Serrate mediated signaling involves other regions of Notch.

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Organizational Affiliation: 

Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom; [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NEUROGENIC LOCUS NOTCH HOMOLOG PROTEIN 1	A	135	Homo sapiens	Mutation(s): 0  Gene Names: NOTCH1, TAN1
Find proteins for P46531 (Homo sapiens) Explore P46531  Go to UniProtKB:  P46531
NIH Common Fund Data Resources
PHAROS:  P46531 GTEx:  ENSG00000148400

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-alpha-L-fucopyranose	B	2		O-Glycosylation

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	A	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.61 Å
• R-Value Free: 0.270 
• R-Value Work: 0.231 
• R-Value Observed: 0.232 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 28.44	α = 90
b = 28.44	β = 90
c = 282.39	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
xia2	data reduction
xia2	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2014-04-25 
• Released Date: 2014-05-21 
Deposition Author(s): Taylor, P., Takeuchi, H., Sheppard, D., Chillakuri, C., Lea, S.M., Haltiwanger, R.S., Handford, P.A.

Revision History  

• Version 1.0: 2014-05-21
  Type: Initial release
  
• Version 1.1: 2014-06-04
  Changes: Database references
• Version 1.2: 2018-02-07
  Changes: Structure summary
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Other, Structure summary