PDBsum entry 2es3

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protein Protein-protein interface(s) links
Sugar binding protein PDB id
Jmol PyMol
Protein chain
209 a.a. *
Waters ×257
* Residue conservation analysis
PDB id:
Name: Sugar binding protein
Title: Crystal structure of thrombospondin-1 n-terminal domain in p1 form at 1.85a resolution
Structure: Thrombospondin-1. Chain: a, b. Fragment: n-terminal domain. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: thbs1, tsp, tsp1. Expressed in: drosophila melanogaster. Expression_system_taxid: 7227. Expression_system_cell_line: s2 cell.
1.85Å     R-factor:   0.190     R-free:   0.250
Authors: K.Tan,J.Wang,J.Lawler
Key ref:
K.Tan et al. (2007). Heparin-induced cis- and trans- dimerization modes of the thrombospondin-1 N-terminal domain. J Biol Chem, 283, 3932-3941. PubMed id: 18065761 DOI: 10.1074/jbc.M705203200
25-Oct-05     Release date:   31-Oct-06    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
P07996  (TSP1_HUMAN) -  Thrombospondin-1
1170 a.a.
209 a.a.*
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     extracellular space   1 term 
  Biological process     inflammatory response   2 terms 
  Biochemical function     extracellular matrix binding     2 terms  


DOI no: 10.1074/jbc.M705203200 J Biol Chem 283:3932-3941 (2007)
PubMed id: 18065761  
Heparin-induced cis- and trans- dimerization modes of the thrombospondin-1 N-terminal domain.
K.Tan, M.Duquette, J.H.Liu, K.Shanmugasundaram, A.Joachimiak, J.T.Gallagher, A.C.Rigby, J.H.Wang, J.Lawler.
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 (1) dp8 and dp10 bind to TSPN-1 in a manner similar to Arixtra, and (2) 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 enhance 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.
  Selected figure(s)  
Figure 2.
FIGURE 2. Docked structure of dp10 heparin in complex with TSPN-1. A, TSPN-1·dp10 low energy complex identified using AutoDock4. TSPN-1 residues involved in the hydrogen bonding network are rendered in ball-and-stick. Each residue involved in the hydrogen bonding network is annotated. For clarity hydrogen bonds are not displayed. Each domain is labeled and rendered as a ribbon drawing, with -helices colored green (domain A) or magenta (domain B), and β-strands and random coil are colored cyan (domain A) or yellow (domain B). The heparin moiety dp10 is rendered in ball and stick representation. B, Molcad surface of the TSPN-1·dp10 complex with residues involved in the hydrogen bonding network colored in blue. This view of the TSPN-1·dp10 complex is the result of rotating the complex –90° around the x-axis (out of the plane of the page or screen) to provide a view of this complex from the heparin binding site, which is located at the base of complex in panel A. Figs. 2B and 4B were prepared using the SYBYL suite of programs (Tripos).
Figure 5.
FIGURE 5. The native TSPN-1 structure in P1 space group. A, a ribbon drawing of the two TSPN-1 domains in one asymmetric unit. They are not related by any pseudo-symmetric operation. Residue Arg-42 from the major heparin-binding site of each domain is drawn in ball-and-stick form. The two TSPN-1 domains interact with each other extensively through their edge strands (see "Results"). The electric dipole moment of the two TSPN-1 domains is shown by the blue arrow and centered at the beginning of the arrow. B, an electrostatic potential surface representation of the two TSPN-1 domains in the native TSPN-1 structure. Residue Arg-42 from the major heparin-binding site of each TSPN-1 domain is labeled to show the separation of the two major heparin-binding sites in this native structure. The orientation of the figure is similar to the one shown in panel A.
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2007, 283, 3932-3941) copyright 2007.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19276170 K.Tan, M.Duquette, A.Joachimiak, and J.Lawler (2009).
The crystal structure of the signature domain of cartilage oligomeric matrix protein: implications for collagen, glycosaminoglycan and integrin binding.
  FASEB J, 23, 2490-2501.
PDB code: 3fby
19706610 Y.Liu, and D.F.Mosher (2009).
Interactions among stalk modules of thrombospondin-1.
  J Biol Chem, 284, 28563-28570.  
19172746 K.Singh, A.G.Gittis, P.Nguyen, D.C.Gowda, L.H.Miller, and D.N.Garboczi (2008).
Structure of the DBL3x domain of pregnancy-associated malaria protein VAR2CSA complexed with chondroitin sulfate A.
  Nat Struct Mol Biol, 15, 932-938.
PDB codes: 3cml 3cpz
18602404 K.Tan, M.Duquette, J.H.Liu, J.Lawler, and J.H.Wang (2008).
The crystal structure of the heparin-binding reelin-N domain of f-spondin.
  J Mol Biol, 381, 1213-1223.
PDB code: 3coo
18359766 N.Fukuhara, J.A.Howitt, S.A.Hussain, and E.Hohenester (2008).
Structural and functional analysis of slit and heparin binding to immunoglobulin-like domains 1 and 2 of Drosophila Robo.
  J Biol Chem, 283, 16226-16234.
PDB codes: 2vr9 2vra
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