1DY0

Murine endostatin, crystal form II


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.208 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Variable Zinc Coordination in Endostatin

Hohenester, E.Sasaki, T.Mann, K.Timpl, R.

(2000) J Mol Biol 297: 1

  • DOI: 10.1006/jmbi.2000.3553
  • Primary Citation of Related Structures:  
    1DY1, 1DY0

  • PubMed Abstract: 
  • Endostatin is a proteolytic fragment of collagen XVIII that potently inhibits angiogenesis and tumour growth. Human endostatin contains a zinc ion, bound near the N terminus, which was not observed in the original structure of mouse endostatin at pH ...

    Endostatin is a proteolytic fragment of collagen XVIII that potently inhibits angiogenesis and tumour growth. Human endostatin contains a zinc ion, bound near the N terminus, which was not observed in the original structure of mouse endostatin at pH 5. Controversial data exist on the role of this zinc ion in the anti-tumour activity. We report two new crystal structures of mouse endostatin at pH 8.5 with bound zinc. One crystal form shows a metal ion coordination similar to that in human endostatin (His132, His134, His142, Asp207), but the conformation of the N-terminal segment is different. In the other crystal form, Asp136 replaces His132 as a zinc ligand. Site-directed mutagenesis of zinc-binding residues demonstrates that both coordination geometries occur in solution. The large degree of structural heterogeneity of the zinc-binding site has implications for endostatin function. We conclude that zinc is likely to play a structural rather than a critical functional role in endostatin.


    Related Citations: 
    • Crystal Structure of the Angiogenesis Inhibitor Endostatin at 1.5 Angstrom Resolution
      Hohenester, E., Sasaki, T., Olsen, B.R., Timpl, R.
      (1998) EMBO J 17: 1656

    Organizational Affiliation

    Biophysics Section, Blackett Laboratory, Imperial College, London, SW7 2AZ, UK. hohenester@ic.ac.uk



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
COLLAGEN ALPHA1(XVIII) CHAINA188Mus musculusMutation(s): 2 
Gene Names: Col18a1
Find proteins for P39061 (Mus musculus)
Explore P39061 
Go to UniProtKB:  P39061
NIH Common Fund Data Resources
IMPC  MGI:88451
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.208 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.81α = 90
b = 62.81β = 90
c = 88.07γ = 90
Software Package:
Software NamePurpose
X-PLORrefinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-04-11
    Type: Initial release
  • Version 1.1: 2011-05-07
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-06-28
    Changes: Advisory, Data collection
  • Version 1.4: 2019-05-22
    Changes: Data collection, Refinement description