Laminin G like domain 3 from human perlecan

Experimental Data Snapshot

  • Resolution: 1.50 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.179 

wwPDB Validation   3D Report Full Report

This is version 1.1 of the entry. See complete history


Crystal Structure of the LG3 Domain of Endorepellin, an Angiogenesis Inhibitor.

Van Le, B.Kim, H.Choi, J.Kim, J.H.Hahn, M.J.Lee, C.Kim, K.K.Hwang, H.Y.

(2011) J Mol Biol 414: 231-242

  • DOI: https://doi.org/10.1016/j.jmb.2011.09.048
  • Primary Citation of Related Structures:  
    3SH4, 3SH5

  • PubMed Abstract: 

    Endorepellin, the C-terminal region of perlecan, inhibits angiogenesis by disrupting actin cytoskeleton and focal adhesions. The C-terminal laminin-like globular domain (LG3) of endorepellin directs most of this antiangiogenic activity. To investigate the angiostatic mechanism and to identify structural determinants, we have solved crystal structures of the LG3 domain in both apo- and calcium-bound forms at resolutions of 1.5 Å and 2.8 Å, respectively. The conserved core has the jellyroll fold characteristic of LG domains. The calcium-induced structural changes seem very restricted, and the calcium binding site appears to be preformed, suggesting that the bound calcium ion, rather than structural rearrangements, contributes to antiangiogenesis. We have identified H4268 on the EF loop as a key residue for the biochemical function of LG3, since its mutation abolishes antiangiogenic activity, and mutant LG3 can no longer form a direct interaction with integrin. Taken together, we propose that these two distinct structural elements contribute to the angiostatic effect of endorepellin.

  • Organizational Affiliation

    Department of Molecular Cell Biology, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Suwon 440-746, Korea.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
LG3 peptide195Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P98160 (Homo sapiens)
Explore P98160 
Go to UniProtKB:  P98160
PHAROS:  P98160
GTEx:  ENSG00000142798 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP98160
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.50 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.179 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 39.95α = 90
b = 54.655β = 90
c = 64.353γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-12-14
    Type: Initial release
  • Version 1.1: 2017-11-08
    Changes: Refinement description