4XLW

Complex of Notch1 (EGF11-13) bound to Delta-like 4 (N-EGF2)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.39 Å
  • R-Value Free: 0.310 
  • R-Value Work: 0.257 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Structural biology. Structural basis for Notch1 engagement of Delta-like 4.

Luca, V.C.Jude, K.M.Pierce, N.W.Nachury, M.V.Fischer, S.Garcia, K.C.

(2015) Science 347: 847-853

  • DOI: 10.1126/science.1261093
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Notch receptors guide mammalian cell fate decisions by engaging the proteins Jagged and Delta-like (DLL). The 2.3 angstrom resolution crystal structure of the interacting regions of the Notch1-DLL4 complex reveals a two-site, antiparallel binding ori ...

    Notch receptors guide mammalian cell fate decisions by engaging the proteins Jagged and Delta-like (DLL). The 2.3 angstrom resolution crystal structure of the interacting regions of the Notch1-DLL4 complex reveals a two-site, antiparallel binding orientation assisted by Notch1 O-linked glycosylation. Notch1 epidermal growth factor-like repeats 11 and 12 interact with the DLL4 Delta/Serrate/Lag-2 (DSL) domain and module at the N-terminus of Notch ligands (MNNL) domains, respectively. Threonine and serine residues on Notch1 are functionalized with O-fucose and O-glucose, which act as surrogate amino acids by making specific, and essential, contacts to residues on DLL4. The elucidation of a direct chemical role for O-glycans in Notch1 ligand engagement demonstrates how, by relying on posttranslational modifications of their ligand binding sites, Notch proteins have linked their functional capacity to developmentally regulated biosynthetic pathways.


    Organizational Affiliation

    Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA. Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA. Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Neurogenic locus notch homolog protein 1
A, C, E, G
124Rattus norvegicusMutation(s): 0 
Gene Names: Notch1
Find proteins for Q07008 (Rattus norvegicus)
Go to UniProtKB:  Q07008
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Delta-like protein
B, D, F, H
261Rattus norvegicusMutation(s): 4 
Gene Names: Dll4
Find proteins for D3ZHH1 (Rattus norvegicus)
Go to UniProtKB:  D3ZHH1
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
A, C, E, G
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
BGC
Query on BGC

Download SDF File 
Download CCD File 
A, C, E, G
BETA-D-GLUCOSE
C6 H12 O6
WQZGKKKJIJFFOK-VFUOTHLCSA-N
 Ligand Interaction
FUC
Query on FUC

Download SDF File 
Download CCD File 
A, C, E, G
ALPHA-L-FUCOSE
C6 H12 O5
SHZGCJCMOBCMKK-SXUWKVJYSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
B, D, F, H
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MLY
Query on MLY
B, D, F, H
L-PEPTIDE LINKINGC8 H18 N2 O2LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.39 Å
  • R-Value Free: 0.310 
  • R-Value Work: 0.257 
  • Space Group: P 1 21 1
  • Diffraction Data DOI: 
    10.15785/SBGRID/69 SBGrid
Unit Cell:
Length (Å)Angle (°)
a = 84.560α = 90.00
b = 95.570β = 96.21
c = 122.900γ = 90.00
Software Package:
Software NamePurpose
XSCALEdata scaling
PHENIXrefinement
PHASERphasing
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesNIH-1RO1-GM097015

Revision History 

  • Version 1.0: 2015-03-04
    Type: Initial release
  • Version 1.1: 2015-03-11
    Type: Database references
  • Version 1.2: 2015-05-27
    Type: Refinement description
  • Version 1.3: 2015-06-10
    Type: Refinement description
  • Version 1.4: 2017-09-20
    Type: Author supporting evidence, Derived calculations, Source and taxonomy