1LSL | pdb_00001lsl

Crystal Structure of the Thrombospondin-1 Type 1 Repeats

• PDB DOI: https://doi.org/10.2210/pdb1LSL/pdb

• Classification: CELL ADHESION
• Organism(s): Homo sapiens
• Expression System: Drosophila
• Mutation(s): No 


• Deposited: 2002-05-17 Released: 2002-12-18 
• Deposition Author(s): Tan, K., Duquette, M., Liu, J., Dong, Y., Zhang, R., Joachimiak, A., Lawler, J., Wang, J.-H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.282 (Depositor) 
• R-Value Work: 
  0.238 (Depositor) 
• R-Value Observed: 
  0.235 (Depositor) 

Literature

Crystal structure of the TSP-1 type 1 repeats: a novel layered fold and its biological implication.

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

(2002) J Cell Biol 159: 373-382

• PubMed: 12391027 
• DOI: https://doi.org/10.1083/jcb.200206062
• Primary Citation Related Structures: 
  1LSL


• PubMed Abstract: 
  

  Thrombospondin-1 (TSP-1) contains three type 1 repeats (TSRs), which mediate cell attachment, glycosaminoglycan binding, inhibition of angiogenesis, activation of TGFbeta, and inhibition of matrix metalloproteinases. The crystal structure of the TSRs reported in this article reveals a novel, antiparallel, three-stranded fold that consists of alternating stacked layers of tryptophan and arginine residues from respective strands, capped by disulfide bonds on each end. The front face of the TSR contains a right-handed spiral, positively charged groove that might be the "recognition" face, mediating interactions with various ligands. This is the first high-resolution crystal structure of a TSR domain that provides a prototypic architecture for structural and functional exploration of the diverse members of the TSR superfamily.

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Organizational Affiliation: 
• Dana-Farber Cancer Institute, Harvard Medical School, 44 Binney Street, Boston, MA 02115, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 12.5 kDa 
• Atom Count: 1,018 
• Modeled Residue Count: 113 
• Deposited Residue Count: 113 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thrombospondin 1	A	113	Homo sapiens	Mutation(s): 0  Gene Names: THBS1
UniProt & NIH Common Fund Data Resources
Find proteins for P07996 (Homo sapiens) Explore P07996  Go to UniProtKB:  P07996
PHAROS:  P07996 GTEx:  ENSG00000137801
Glycosylation
Glycosylation Sites: 1		Go to GlyGen: P07996-1

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FUC	C [auth A]	alpha-L-fucopyranose C6 H12 O5 SHZGCJCMOBCMKK-SXUWKVJYSA-N
FUL	B [auth A]	beta-L-fucopyranose C6 H12 O5 SHZGCJCMOBCMKK-KGJVWPDLSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.282 (Depositor) 
• R-Value Work:  0.238 (Depositor) 
• R-Value Observed: 0.235 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.63	α = 90
b = 84.41	β = 108.67
c = 37.17	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
HKL-2000	data reduction
MLPHARE	phasing
X-PLOR	refinement
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2002-12-18 
Deposition Author(s): Tan, K., Duquette, M., Liu, J., Dong, Y., Zhang, R., Joachimiak, A., Lawler, J., Wang, J.-H.

Revision History  

• Version 1.0: 2002-12-18
  Type: Initial release
  
• Version 1.1: 2008-04-28
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Data collection, Derived calculations, Structure summary
• Version 1.4: 2024-10-30
  Changes: Data collection, Database references, Structure summary