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: 15.13 kDa 
• Atom Count: 928 
• Modelled Residue Count: 120 
• Deposited Residue Count: 135 
• Unique protein chains: 1

2VJ3

Human Notch-1 EGFs 11-13

• PDB DOI: 10.2210/pdb2VJ3/pdb

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


• Deposited: 2007-12-06 Released: 2008-07-29 
• Deposition Author(s): Johnson, S., Cordle, J., Tay, J.Z., Roversi, P., Lea, S.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.244 
• R-Value Work: 0.239 
• R-Value Observed: 0.239 

Literature

A Conserved Face of the Jagged/Serrate Dsl Domain is Involved in Notch Trans-Activation and Cis-Inhibition.

Cordle, J., Johnson, S., Tay, J.Z., Roversi, P., Wilkin, M.B., De Madrid, B.H., Shimizu, H., Jensen, S., Whiteman, P., Jin, B., Redfield, C., Baron, M., Lea, S.M., Handford, P.A.

(2008) Nat Struct Mol Biol 15: 849

• PubMed: 18660822 
• DOI: 10.1038/nsmb.1457
• Primary Citation of Related Structures:  
  2VJ2, 2VJ3


• PubMed Abstract: 
  

The Notch receptor and its ligands are key components in a core metazoan signaling pathway that regulates the spatial patterning, timing and outcome of many cell-fate decisions. Ligands contain a disulfide-rich Delta/Serrate/LAG-2 (DSL) domain required for Notch trans-activation or cis-inhibition. Here we report the X-ray structure of a receptor binding region of a Notch ligand, the DSL-EGF3 domains of human Jagged-1 (J-1(DSL-EGF3)). The structure reveals a highly conserved face of the DSL domain, and we show, by functional analysis of Drosophila melanogster ligand mutants, that this surface is required for both cis- and trans-regulatory interactions with Notch. We also identify, using NMR, a surface of Notch-1 involved in J-1(DSL-EGF3) binding. Our data imply that cis- and trans-regulation may occur through the formation of structurally distinct complexes that, unexpectedly, involve the same surfaces on both ligand and receptor.

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Organizational Affiliation: 

Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK.

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
UniProt & NIH Common Fund Data Resources
Find proteins for P46531 (Homo sapiens) Explore P46531  Go to UniProtKB:  P46531
PHAROS:  P46531

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	B [auth A], C [auth A], D [auth A], E [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL	H [auth A], I [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	F [auth A], G [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.244 
• R-Value Work: 0.239 
• R-Value Observed: 0.239 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 28	α = 90
b = 28	β = 90
c = 281.7	γ = 120

Software Package:

Software Name	Purpose
TNT	refinement
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2007-12-06 
• Released Date: 2008-07-29 
Deposition Author(s): Johnson, S., Cordle, J., Tay, J.Z., Roversi, P., Lea, S.M.

Revision History  

• Version 1.0: 2008-07-29
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-07-05
  Changes: Data collection