1YO8 | pdb_00001yo8

Structure of the C-terminal domain of human thrombospondin-2

• PDB DOI: https://doi.org/10.2210/pdb1YO8/pdb

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


• Deposited: 2005-01-26 Released: 2005-09-27 
• Deposition Author(s): Carlson, C.B., Bernstein, D.A., Annis, D.S., Misenheimer, T.M., Hannah, B.A., Mosher, D.F., Keck, J.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.284 (Depositor), 0.275 (DCC) 
• R-Value Work: 
  0.218 (Depositor), 0.216 (DCC) 
• R-Value Observed: 
  0.224 (Depositor) 

Literature

Structure of the calcium-rich signature domain of human thrombospondin-2

Carlson, C.B., Bernstein, D.A., Annis, D.S., Misenheimer, T.M., Hannah, B.L., Mosher, D.F., Keck, J.L.

(2005) Nat Struct Mol Biol 12: 910-914

• PubMed: 16186819 
• DOI: https://doi.org/10.1038/nsmb997
• Primary Citation Related Structures: 
  1YO8


• PubMed Abstract: 
  

  Thrombospondins (THBSs) are secreted glycoproteins that have key roles in interactions between cells and the extracellular matrix. Here, we describe the 2.6-A-resolution crystal structure of the glycosylated signature domain of human THBS2, which includes three epidermal growth factor-like modules, 13 aspartate-rich repeats and a lectin-like module. These elements interact extensively to form three structural regions termed the stalk, wire and globe. The THBS2 signature domain is stabilized by these interactions and by a network of 30 bound Ca(2+) ions and 18 disulfide bonds. The structure suggests how genetic alterations of THBSs result in disease.

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Organizational Affiliation: 
• Department of Medicine, 4285B Medical Sciences Center, University of Wisconsin-Madison, 1300 University Avenue, Madison, Wisconsin 53706, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 73.53 kDa 
• Atom Count: 5,085 
• Modeled Residue Count: 621 
• Deposited Residue Count: 634 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
thrombospondin-2	A	634	Homo sapiens	Mutation(s): 5  Gene Names: THBS2, TSP2
UniProt & NIH Common Fund Data Resources
Find proteins for P35442 (Homo sapiens) Explore P35442  Go to UniProtKB:  P35442
PHAROS:  P35442 GTEx:  ENSG00000186340
Glycosylation
Glycosylation Sites: 4		Go to GlyGen: P35442-1

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	B	3		N-Glycosylation
Glycosylation Resources
GlyTouCan: G62182OO GlyCosmos: G62182OO GlyGen: G62182OO

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C	2		N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	D [auth A], E [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
CA	AA [auth A], BA [auth A], CA [auth A], DA [auth A], EA [auth A], F [auth A], FA [auth A], G [auth A], GA [auth A], H [auth A], HA [auth A], I [auth A], IA [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], P [auth A], Q [auth A], R [auth A], S [auth A], T [auth A], U [auth A], V [auth A], W [auth A], X [auth A], Y [auth A], Z [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.284 (Depositor), 0.275 (DCC) 
• R-Value Work:  0.218 (Depositor), 0.216 (DCC) 
• R-Value Observed: 0.224 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 93.437	α = 90
b = 121.588	β = 90
c = 155.33	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
SCALEPACK	data scaling
SOLVE	phasing
REFMAC	refinement
HKL-2000	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-09-27 
Deposition Author(s): Carlson, C.B., Bernstein, D.A., Annis, D.S., Misenheimer, T.M., Hannah, B.A., Mosher, D.F., Keck, J.L.

Revision History  

• Version 1.0: 2005-09-27
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary
• Version 2.1: 2024-11-20
  Changes: Data collection, Database references, Structure summary