4D90

Crystal Structure of Del-1 EGF domains


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.601 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.204 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The RGD finger of Del-1 is a unique structural feature critical for integrin binding.

Schurpf, T.Chen, Q.Liu, J.H.Wang, R.Springer, T.A.Wang, J.H.

(2012) Faseb J. 26: 3412-3420

  • DOI: 10.1096/fj.11-202036

  • PubMed Abstract: 
  • Developmental endothelial cell locus-1 (Del-1) glycoprotein is secreted by endothelial cells and a subset of macrophages. Del-1 plays a regulatory role in vascular remodeling and functions in innate immunity through interaction with integrin α(V)β(3) ...

    Developmental endothelial cell locus-1 (Del-1) glycoprotein is secreted by endothelial cells and a subset of macrophages. Del-1 plays a regulatory role in vascular remodeling and functions in innate immunity through interaction with integrin α(V)β(3). Del-1 contains 3 epidermal growth factor (EGF)-like repeats and 2 discoidin-like domains. An Arg-Gly-Asp (RGD) motif in the second EGF domain (EGF2) mediates adhesion by endothelial cells and phagocytes. We report the crystal structure of its 3 EGF domains. The RGD motif of EGF2 forms a type II' β turn at the tip of a long protruding loop, dubbed the RGD finger. Whereas EGF2 and EGF3 constitute a rigid rod via an interdomain calcium ion binding site, the long linker between EGF1 and EGF2 lends considerable flexibility to EGF1. Two unique O-linked glycans and 1 N-linked glycan locate to the opposite side of EGF2 from the RGD motif. These structural features favor integrin binding of the RGD finger. Mutagenesis data confirm the importance of having the RGD motif at the tip of the RGD finger. A database search for EGF domain sequences shows that this RGD finger is likely an evolutionary insertion and unique to the EGF domain of Del-1 and its homologue milk fat globule-EGF 8.


    Organizational Affiliation

    Immune Disease Institute, Harvard Medical School, Boston, MA, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
EGF-like repeat and discoidin I-like domain-containing protein 3
A, B
143Homo sapiensMutation(s): 0 
Gene Names: EDIL3 (DEL1)
Find proteins for O43854 (Homo sapiens)
Go to Gene View: EDIL3
Go to UniProtKB:  O43854
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
A, B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
FUC
Query on FUC

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

Download SDF File 
Download CCD File 
A, B
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
NGA
Query on NGA

Download SDF File 
Download CCD File 
A, B
N-ACETYL-D-GALACTOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-JAJWTYFOSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.601 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.204 
  • Space Group: P 32
Unit Cell:
Length (Å)Angle (°)
a = 82.680α = 90.00
b = 82.680β = 90.00
c = 56.422γ = 120.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PHENIXrefinement
HKL-2000data collection
HKL-2000data scaling
PHASERphasing
DENZOdata reduction
PDB_EXTRACTdata extraction
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-05-30
    Type: Initial release
  • Version 1.1: 2013-01-02
    Type: Database references
  • Version 1.2: 2017-11-15
    Type: Refinement description