3SH4 | pdb_00003sh4

Laminin G like domain 3 from human perlecan


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 
    0.213 (Depositor), 0.216 (DCC) 
  • R-Value Work: 
    0.177 (Depositor) 
  • R-Value Observed: 
    0.179 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 3SH4

This is version 1.2 of the entry. See complete history

Literature

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 Biology 414: 231-242

  • DOI: https://doi.org/10.1016/j.jmb.2011.09.048
  • Primary Citation 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.

Macromolecule Content 

  • Total Structure Weight: 20.57 kDa 
  • Atom Count: 1,653 
  • Modeled Residue Count: 195 
  • Deposited Residue Count: 195 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  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
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free:  0.213 (Depositor), 0.216 (DCC) 
  • R-Value Work:  0.177 (Depositor) 
  • R-Value Observed: 0.179 (Depositor) 
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
REFMACrefinement
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
  • Version 1.2: 2024-11-06
    Changes: Data collection, Database references, Structure summary