PDBsum entry 2erf

Sugar binding protein

PDB id: 2erf

Contents

Protein chain

209 a.a. *

Waters ×217

* Residue conservation analysis

PDB id:

2erf

Name:

Sugar binding protein

Title:

Crystal structure of the thrombospondin-1 n-terminal domain at 1.45a resolution

Structure:

Thrombospondin-1. Chain: a. 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.

Resolution:

1.45Å R-factor: 0.186 R-free: 0.217

Authors:

K.Tan,J.Wang,J.Lawler

Key ref:

K.Tan et al. (2006). The structures of the thrombospondin-1 N-terminal domain and its complex with a synthetic pentameric heparin. Structure, 14, 33-42. PubMed id: 16407063 DOI: 10.1016/j.str.2005.09.017

Date:

24-Oct-05 Release date: 17-Jan-06

Protein chain

P07996  (TSP1_HUMAN) -  Thrombospondin-1 from Homo sapiens

Seq: 1170 a.a.

Struc: 209 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

DOI no: 10.1016/j.str.2005.09.017

Structure 14:33-42 (2006)

PubMed id: 16407063

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

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

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.

Selected figure(s)

Figure 4.
Figure 4. The Topology of TSPN-1
The topology of (A) TSPN-1 is compared with that of (B) CTSP-1 (the C-terminal domain of TSP-1) (Kvansakul et al., 2004) and (C) a typical LG (Laminin A G-domain [LG]/Neurexin/Sex hormone binding globulin [SHBG]) repeat (Rudenko et al., 2001). For the LG structure, only the common positions of the b strands are shown. The disulfide bonds are highlighted in yellow. Only b strands (cyan) are labeled for comparison. The a helices of TSPN-1 and CTSP-1 are shown in green. The two structures can't be simply superimposed. The best alignment can only be made with the middle strands of the back sheet, b14, b5, b10, and b11 of TSPN-1 and b15, b5, b11, and b12 of CTSP-1. Even in this alignment, the b strands from the two front sheets shift over about one strand and also rotate slightly. The edge strands, especially the N-terminal edge strands, are totally out of alignment. The front concaved sheet of CTSP-1 is distinctly curved, while that of TSPN-1 is relatively flat.

The above figure is reprinted by permission from Cell Press: Structure (2006, 14, 33-42) copyright 2006.

Figure was selected by the author.