Murine endostatin, crystal form II

Experimental Data Snapshot

  • Resolution: 2.20 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.208 

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This is version 1.5 of the entry. See complete history


Variable Zinc Coordination in Endostatin

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

(2000) J Mol Biol 297: 1

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

  • 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 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.

  • Organizational Affiliation

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

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
COLLAGEN ALPHA1(XVIII) CHAIN188Mus musculusMutation(s): 2 
UniProt & NIH Common Fund Data Resources
Find proteins for P39061 (Mus musculus)
Explore P39061 
Go to UniProtKB:  P39061
IMPC:  MGI:88451
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP39061
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • 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
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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
  • Version 1.5: 2023-12-06
    Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description