Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | 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: 13.68 kDa 
• Atom Count: 1024 
• Modelled Residue Count: 115 
• Deposited Residue Count: 116 
• Unique protein chains: 1

7ALJ

Structure of Drosophila Notch EGF domains 11-13

• PDB DOI: 10.2210/pdb7ALJ/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Drosophila melanogaster
• Expression System: Drosophila melanogaster
• Mutation(s): No 


• Deposited: 2020-10-06 Released: 2021-08-04 
• Deposition Author(s): Suckling, R., Johnson, S., Lea, S.M.
• Funding Organization(s): Medical Research Council (MRC, United Kingdom), Wellcome Trust

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.52 Å
• R-Value Free: 0.241 
• R-Value Work: 0.201 
• R-Value Observed: 0.203 

Literature

The conserved C2 phospholipid-binding domain in Delta contributes to robust Notch signalling.

Martins, T., Meng, Y., Korona, B., Suckling, R., Johnson, S., Handford, P.A., Lea, S.M., Bray, S.J.

(2021) EMBO Rep 22: e52729-e52729

• PubMed: 34347930 
• DOI: 10.15252/embr.202152729
• Primary Citation of Related Structures:  
  7ALJ, 7ALK, 7ALT


• PubMed Abstract: 
  

Accurate Notch signalling is critical for development and homeostasis. Fine-tuning of Notch-ligand interactions has substantial impact on signalling outputs. Recent structural studies have identified a conserved N-terminal C2 domain in human Notch ligands which confers phospholipid binding in vitro. Here, we show that Drosophila ligands Delta and Serrate adopt the same C2 domain structure with analogous variations in the loop regions, including the so-called β1-2 loop that is involved in phospholipid binding. Mutations in the β1-2 loop of the Delta C2 domain retain Notch binding but have impaired ability to interact with phospholipids in vitro. To investigate its role in vivo, we deleted five residues within the β1-2 loop of endogenous Delta. Strikingly, this change compromises ligand function. The modified Delta enhances phenotypes produced by Delta loss-of-function alleles and suppresses that of Notch alleles. As the modified protein is present on the cell surface in normal amounts, these results argue that C2 domain phospholipid binding is necessary for robust signalling in vivo fine-tuning the balance of trans and cis ligand-receptor interactions.

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Organizational Affiliation: 

Department of Physiology Development and Neuroscience, University of Cambridge, Cambridge, UK.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Neurogenic locus Notch protein	A	116	Drosophila melanogaster	Mutation(s): 0  Gene Names: N, CG3936
UniProt
Find proteins for P07207 (Drosophila melanogaster) Explore P07207  Go to UniProtKB:  P07207

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
beta-D-xylopyranose-(1-3)-beta-D-glucopyranose	B	2		O-Glycosylation

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	G [auth A], H [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
BGC	F [auth A]	beta-D-glucopyranose C6 H12 O6 WQZGKKKJIJFFOK-VFUOTHLCSA-N
FUC	E [auth A]	alpha-L-fucopyranose C6 H12 O5 SHZGCJCMOBCMKK-SXUWKVJYSA-N
CA	C [auth A], D [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.52 Å
• R-Value Free: 0.241 
• R-Value Work: 0.201 
• R-Value Observed: 0.203 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 180.82	α = 90
b = 31.286	β = 90.769
c = 21.795	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PHENIX	refinement
xia2	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2020-10-06 
• Released Date: 2021-08-04 
Deposition Author(s): Suckling, R., Johnson, S., Lea, S.M.

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Funding Organization	Location	Grant Number
Medical Research Council (MRC, United Kingdom)	United Kingdom	MR/L001187/1
Medical Research Council (MRC, United Kingdom)	United Kingdom	MR-R009317/1
Wellcome Trust	United Kingdom	100298

Revision History  

• Version 1.0: 2021-08-04
  Type: Initial release
  
• Version 1.1: 2021-10-13
  Changes: Data collection, Database references