9B3N

Human Notch-1 EGFs 20-24

• PDB DOI: https://doi.org/10.2210/pdb9B3N/pdb

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


• Deposited: 2024-03-19 Released: 2024-10-16 
• Deposition Author(s): Johnson, S., Suckling, R., Handford, P.A., 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: 1.50 Å
• R-Value Free: 0.198 
• R-Value Work: 0.175 
• R-Value Observed: 0.177 

Starting Model: experimental

Literature

Structural and functional studies of the EGF20-27 region reveal new features of the human Notch receptor important for optimal activation

Bo, Z., Rowntree, T., Johnson, S., Nurmandi, H., Suckling, R., Hill, J., Korona, B., Weisshuhn, P., Sheppard, D., Meng, Y., Liang, S., Lowe, E., Lea, S.M., Redfield, C., Handford, P.A.

To be published.

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 22.85 kDa 
• Atom Count: 1,810 
• Modelled Residue Count: 195 
• Deposited Residue Count: 201 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Neurogenic locus notch homolog protein 1	A	201	Homo sapiens	Mutation(s): 0  Gene Names: NOTCH1, TAN1
UniProt & NIH Common Fund Data Resources
Find proteins for P46531 (Homo sapiens) Explore P46531  Go to UniProtKB:  P46531
PHAROS:  P46531 GTEx:  ENSG00000148400
Glycosylation
Glycosylation Sites: 6		Go to GlyGen: P46531-1

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
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
BGC	C [auth A]	beta-D-glucopyranose C6 H12 O6 WQZGKKKJIJFFOK-VFUOTHLCSA-N
FUC	D [auth A], E [auth A], F [auth A], G [auth A]	alpha-L-fucopyranose C6 H12 O5 SHZGCJCMOBCMKK-SXUWKVJYSA-N
EDO	L [auth A], M [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CA (Subject of Investigation/LOI)	H [auth A], I [auth A], J [auth A], K [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.198 
• R-Value Work: 0.175 
• R-Value Observed: 0.177 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 28.03	α = 99.71
b = 35.08	β = 92.35
c = 63.89	γ = 96.86

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-10-16 
Deposition Author(s): Johnson, S., Suckling, R., Handford, P.A., Lea, S.M.

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Funding Organization	Location	Grant Number
Medical Research Council (MRC, United Kingdom)	United Kingdom	MR/R009317/1
Medical Research Council (MRC, United Kingdom)	United Kingdom	MR/V008935/1
Wellcome Trust	United Kingdom	100298

Revision History  

• Version 1.0: 2024-10-16
  Type: Initial release