Crystal structure of the Thrombospondin-1 N-terminal domain in complex with fractionated Heparin DP10

Experimental Data Snapshot

  • Resolution: 2.40 Å
  • R-Value Free: 0.296 
  • R-Value Work: 0.253 
  • R-Value Observed: 0.257 

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Heparin-induced cis- and trans-Dimerization Modes of the Thrombospondin-1 N-terminal Domain.

Tan, K.Duquette, M.Liu, J.H.Shanmugasundaram, K.Joachimiak, A.Gallagher, J.T.Rigby, A.C.Wang, J.H.Lawler, J.

(2008) J Biol Chem 283: 3932-3941

  • DOI: https://doi.org/10.1074/jbc.M705203200
  • Primary Citation of Related Structures:  
    2ES3, 2OUH, 2OUJ

  • PubMed Abstract: 

    Through its interactions with proteins and proteoglycans, thrombospondin-1 (TSP-1) functions at the interface of the cell membrane and the extracellular matrix to regulate matrix structure and cellular phenotype. We have previously determined the structure of the high affinity heparin-binding domain of TSP-1, designated TSPN-1, in association with the synthetic heparin, Arixtra. To establish that the binding of TSPN-1 to Arixtra is representative of the association with naturally occurring heparins, we have determined the structures of TSPN-1 in complex with heparin oligosaccharides containing eight (dp8) and ten (dp10) subunits, by x-ray crystallography. We have found that dp8 and dp10 bind to TSPN-1 in a manner similar to Arixtra and that dp8 and dp10 induce the formation of trans and cis TSPN-1 dimers, respectively. In silico docking calculations partnered with our crystal structures support the importance of arginine residues in positions 29, 42, and 77 in binding sulfate groups of the dp8 and dp10 forms of heparin. The ability of several TSPN-1 domains to bind to glycosaminoglycans simultaneously probably increases the affinity of binding through multivalent interactions. The formation of cis and trans dimers of the TSPN-1 domain with relatively short segments of heparin further enhances the ability of TSP-1 to participate in high affinity binding to glycosaminoglycans. Dimer formation may also involve TSPN-1 domains from two separate TSP-1 molecules. This association would enable glycosaminoglycans to cluster TSP-1.

  • Organizational Affiliation

    Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B
251Homo sapiensMutation(s): 1 
Gene Names: THBS1TSPTSP1
UniProt & NIH Common Fund Data Resources
Find proteins for P07996 (Homo sapiens)
Explore P07996 
Go to UniProtKB:  P07996
PHAROS:  P07996
GTEx:  ENSG00000137801 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP07996
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.40 Å
  • R-Value Free: 0.296 
  • R-Value Work: 0.253 
  • R-Value Observed: 0.257 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 40.316α = 90
b = 41.069β = 90
c = 241.779γ = 90
Software Package:
Software NamePurpose
SBC-Collectdata collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-01-08
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2023-08-30
    Changes: Data collection, Database references, Derived calculations, Refinement description