Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 71.37 kDa 
• Atom Count: 5007 
• Residue Count: 622 
• Unique protein chains: 1

2RHP

The Thrombospondin-1 Polymorphism Asn700Ser Associated with Cornoary Artery Disease Causes Local and Long-Ranging Changes in Protein Structure

• DOI: 10.2210/pdb2RHP/pdb

• Classification: CELL ADHESION
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): Yes 


• Deposited: 2007-10-09 Released: 2008-05-27 
• Deposition Author(s): Carlson, C.B., Keck, J.L., Mosher, D.F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 0.277 
• R-Value Work: 0.227 
• R-Value Observed: 0.229 

Literature

Influences of the N700S Thrombospondin-1 Polymorphism on Protein Structure and Stability.

Carlson, C.B., Liu, Y., Keck, J.L., Mosher, D.F.

(2008) J Biol Chem 283: 20069-20076

• PubMed: 18499674 
• DOI: 10.1074/jbc.M800223200
• Primary Citation of Related Structures:  
  2RHP


• PubMed Abstract: 
  

Thrombospondins (THBSs) are multimodular, secreted proteins characterized by a signature domain comprising a unique set of 13 calcium-binding repeats flanked by epidermal growth factor (EGF)-like and lectin-like modules. A polymorphism that changes a conserved Asn to Ser at residue 700 in the most N-terminal calcium-binding repeat of THBS-1 (repeat 1C) is found in 8-10% of European populations and has been linked to increased risk of premature coronary artery disease. The Ser substitution leads to altered stability in the EGF-like and wire modules of the THBS-1 signature domain as assessed by differential scanning calorimetry carried out in 2 mm or 200 mum calcium. Studies of the melting profiles of the THBS-2 signature domain proteins with Asn or Ser at position 702 (homologous to 700 in THBS-1) revealed that the impact of the Ser allele is similar in both THBS-1 and THBS-2. Structure determination of the Ser(702) THBS-2 variant in 2 mm calcium showed that repeat 1C contains two bound calcium ions as in the crystal of the Asn(702) protein, including the ion that is coordinated by Asn(702), and is associated with changes in conformation of repeat 1C and the adjacent EGF-like modules. The Ser substitution leads to the decreased ability of soluble THBS-2 signature domain protein to bind 4B6.13, a conformation-sensitive monoclonal antibody that recognizes an epitope in repeat 1C. These results indicate that although THBS harboring the Ser allele binds a full complement of calcium ions, repeat 1C is altered, leading to destabilization of surrounding structures.

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Organizational Affiliation: 

Department of Medicine and Biomolecular Chemistry, University of Wisconsin, Madison, WI 53706, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thrombospondin-2	A	622	Homo sapiens	Mutation(s): 1  Gene Names: THBS2, TSP2
Find proteins for P35442 (Homo sapiens) Explore P35442  Go to UniProtKB:  P35442
NIH Common Fund Data Resources
PHAROS:  P35442 GTEx:  ENSG00000186340

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	B	2		N-Glycosylation

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	A	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
CA	A	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 0.277 
• R-Value Work: 0.227 
• R-Value Observed: 0.229 
• Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 93.892	α = 90
b = 122.65	β = 90
c = 155.381	γ = 90

Software Package:

Software Name	Purpose
AMoRE	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
DENZO	data reduction
SCALEPACK	data scaling
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2007-10-09 
• Released Date: 2008-05-27 
Deposition Author(s): Carlson, C.B., Keck, J.L., Mosher, D.F.

Revision History 

• Version 1.0: 2008-05-27
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.2: 2017-10-11
  Changes: Data collection, Refinement description
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary