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Structure of a thrombospondin C-terminal fragment reveals a novel calcium core in the type 3 repeats


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.199 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structure of a Thrombospondin C-Terminal Fragment Reveals a Novel Calcium Core in the Type 3 Repeats

Kvansakul, M.Adams, J.C.Hohenester, E.

(2004) Embo J. 23: 1223

  • DOI: 10.1038/sj.emboj.7600166

  • PubMed Abstract: 
  • Thrombospondins (TSPs) are extracellular regulators of cell-matrix interactions and cell phenotype. The most highly conserved region of all TSPs are the calcium-binding type 3 (T3) repeats and the C-terminal globular domain (CTD). The crystal structu ...

    Thrombospondins (TSPs) are extracellular regulators of cell-matrix interactions and cell phenotype. The most highly conserved region of all TSPs are the calcium-binding type 3 (T3) repeats and the C-terminal globular domain (CTD). The crystal structure of a cell-binding TSP-1 fragment, spanning three T3 repeats and the CTD, reveals a compact assembly. The T3 repeats lack secondary structure and are organised around a core of calcium ions; two DxDxDGxxDxxD motifs per repeat each encapsulate two calcium ions in a novel arrangement. The CTD forms a lectin-like beta-sandwich and contains four strictly conserved calcium-binding sites. Disruption of the hairpin structure of T3 repeats 6 and 7 decreases protein secretion and stability. The availability for cell attachment of an RGD motif in T3 repeat 7 is modulated by calcium loading. The central architectural role of calcium explains how it is critical for the functions of the TSP C-terminal region. Mutations in the T3 repeats of TSP-5/COMP, which cause two human skeletal disorders, are predicted to disrupt the tertiary structure of the T3-CTD assembly.


    Organizational Affiliation

    Department of Biological Sciences, Imperial College London, South Kensington Campus, London, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
THROMBOSPONDIN-1
A
350Homo sapiensMutation(s): 2 
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
CA
Query on CA

Download SDF File 
Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.199 
  • Space Group: H 3 2
Unit Cell:
Length (Å)Angle (°)
a = 162.340α = 90.00
b = 162.340β = 90.00
c = 85.140γ = 120.00
Software Package:
Software NamePurpose
CNSrefinement
MOSFLMdata reduction
MLPHAREphasing
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-03-18
    Type: Initial release
  • Version 1.1: 2011-05-07
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-07-12
    Type: Derived calculations