2OUH

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.296 
  • R-Value Work: 0.253 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

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: 10.1074/jbc.M705203200
  • Primary Citation of Related Structures:  

  • 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 str ...

    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Thrombospondin-1
A, B
251Homo sapiensMutation(s): 0 
Gene Names: THBS1 (TSP, TSP1)
Find proteins for P07996 (Homo sapiens)
Go to Gene View: THBS1
Go to UniProtKB:  P07996
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.296 
  • R-Value Work: 0.253 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 40.316α = 90.00
b = 41.069β = 90.00
c = 241.779γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
SBC-Collectdata collection
CNSrefinement
CNSphasing
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-01-08
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance