4XBM

X-ray crystal structure of Notch ligand Delta-like 1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.258 
  • R-Value Observed: 0.260 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.5 of the entry. See complete history


Literature

Notch ligand delta-like1: X-ray crystal structure and binding affinity.

Kershaw, N.J.Church, N.L.Griffin, M.D.Luo, C.S.Adams, T.E.Burgess, A.W.

(2015) Biochem J 468: 159-166

  • DOI: 10.1042/BJ20150010
  • Primary Citation of Related Structures:  
    4XBM

  • PubMed Abstract: 
  • The Notch pathway is a fundamental signalling system in most multicellular animals. We have determined the X-ray crystal structure of the extracellular domain of the Notch ligand delta-like ligand-1 (Dll-1). The structure incorporates the N-terminal C2 domain, receptor-binding DSL domain and the first six (of eight) EGF (epidermal growth factor)-like repeats, which form a highly extended conformation, confirmed by analytical ultracentrifugation ...

    The Notch pathway is a fundamental signalling system in most multicellular animals. We have determined the X-ray crystal structure of the extracellular domain of the Notch ligand delta-like ligand-1 (Dll-1). The structure incorporates the N-terminal C2 domain, receptor-binding DSL domain and the first six (of eight) EGF (epidermal growth factor)-like repeats, which form a highly extended conformation, confirmed by analytical ultracentrifugation. Comparison of our structure with a fragment of Jagged1 ligand allows us to dissect the similarities and differences between the ligand families. Differences in the C2 domains of Dll-1 and Jagged1 suggest their lipid-binding properties are likely to differ. A conserved hydrophobic patch on the surface of both Dll-1 and Jagged1 provides a likely receptor-interaction site that is common to both ligands. We also explore the binding affinity of Dll-1 for a fragment of Notch1 using different techniques. Apparent binding affinities vary when different techniques are used, explaining discrepancies in the literature. Using analytical ultracentrifugation, we perform for the first time binding analyses where both receptor and ligand are in solution, which confirms a Kd of 10 μM for this interaction.


    Organizational Affiliation

    *Department of Structural Biology, Walter and Eliza Hall Institute of Medical Research and Department of Medical Biology, University of Melbourne, Parkville, 3052 Australia.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Delta-like protein 1A, B531Homo sapiensMutation(s): 0 
Gene Names: DLL1UNQ146/PRO172
UniProt & NIH Common Fund Data Resources
Find proteins for O00548 (Homo sapiens)
Explore O00548 
Go to UniProtKB:  O00548
PHAROS:  O00548
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FUC (Subject of Investigation/LOI)
Query on FUC

Download Ideal Coordinates CCD File 
C [auth B]alpha-L-fucopyranose
C6 H12 O5
SHZGCJCMOBCMKK-SXUWKVJYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.258 
  • R-Value Observed: 0.260 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 108.15α = 90
b = 118.87β = 90
c = 134.81γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
PHASERphasing
PDB_EXTRACTdata extraction
XSCALEdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Health and Medical Research Council (NHMRC, Australia)Australia487922

Revision History  (Full details and data files)

  • Version 1.0: 2015-03-11
    Type: Initial release
  • Version 1.1: 2015-05-20
    Changes: Database references
  • Version 1.2: 2015-05-27
    Changes: Data collection, Structure summary
  • Version 1.3: 2017-09-06
    Changes: Author supporting evidence, Data collection, Database references, Derived calculations, Source and taxonomy, Structure summary
  • Version 1.4: 2020-01-08
    Changes: Author supporting evidence, Data collection
  • Version 1.5: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary