Crystal Structure of the Thrombospondin-1 N-terminal domain

Experimental Data Snapshot

  • Resolution: 1.80 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.236 
  • R-Value Observed: 0.237 

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The structures of the thrombospondin-1 N-terminal domain and its complex with a synthetic pentameric heparin.

Tan, K.Duquette, M.Liu, J.H.Zhang, R.Joachimiak, A.Wang, J.H.Lawler, J.

(2006) Structure 14: 33-42

  • DOI: https://doi.org/10.1016/j.str.2005.09.017
  • Primary Citation of Related Structures:  
    1Z78, 1ZA4, 2ERF

  • PubMed Abstract: 

    The N-terminal domain of thrombospondin-1 (TSPN-1) mediates the protein's interaction with (1) glycosaminoglycans, calreticulin, and integrins during cellular adhesion, (2) low-density lipoprotein receptor-related protein during uptake and clearance, and (3) fibrinogen during platelet aggregation. The crystal structure of TSPN-1 to 1.8 A resolution is a beta sandwich with 13 antiparallel beta strands and 1 irregular strand-like segment. Unique structural features of the N- and C-terminal regions, and the disulfide bond location, distinguish TSPN-1 from the laminin G domain and other concanavalin A-like lectins/glucanases superfamily members. The crystal structure of the complex of TSPN-1 with heparin indicates that residues R29, R42, and R77 in an extensive positively charged patch at the bottom of the domain specifically associate with the sulfate groups of heparin. The TSPN-1 structure and identified adjacent linker region provide a structural framework for the analysis of the TSPN domain of various molecules, including TSPs, NELLs, many collagens, TSPEAR, and kielin.

  • 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
Thrombospondin 1215Homo sapiensMutation(s): 0 
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: 1.80 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.236 
  • R-Value Observed: 0.237 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.812α = 90
b = 41.899β = 100.649
c = 53.458γ = 90
Software Package:
Software NamePurpose
HKL-2000data 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: 2006-01-17
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2024-04-03
    Changes: Data collection, Database references, Refinement description