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- PDB-1lsl: Crystal Structure of the Thrombospondin-1 Type 1 Repeats -

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Basic information

Entry
Database: PDB / ID: 1lsl
TitleCrystal Structure of the Thrombospondin-1 Type 1 Repeats
ComponentsThrombospondin 1
KeywordsCELL ADHESION / TSP-1 / TSR
Function / homology
Function and homology information


negative regulation of antigen processing and presentation of peptide or polysaccharide antigen via MHC class II / collagen V binding / thrombospondin complex / endothelial cell-cell adhesion / negative regulation of dendritic cell antigen processing and presentation / positive regulation of extrinsic apoptotic signaling pathway via death domain receptors / negative regulation of sprouting angiogenesis / chronic inflammatory response / negative regulation of endothelial cell chemotaxis / Defective B3GALTL causes PpS ...negative regulation of antigen processing and presentation of peptide or polysaccharide antigen via MHC class II / collagen V binding / thrombospondin complex / endothelial cell-cell adhesion / negative regulation of dendritic cell antigen processing and presentation / positive regulation of extrinsic apoptotic signaling pathway via death domain receptors / negative regulation of sprouting angiogenesis / chronic inflammatory response / negative regulation of endothelial cell chemotaxis / Defective B3GALTL causes PpS / negative regulation of fibroblast growth factor receptor signaling pathway / O-glycosylation of TSR domain-containing proteins / negative regulation of nitric oxide-cGMP mediated signal transduction / negative regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis / negative regulation of long-chain fatty acid import across plasma membrane / positive regulation of transforming growth factor beta1 production / fibrinogen complex / negative regulation of interleukin-12 production / blood coagulation, fibrin clot formation / engulfment of apoptotic cell / low-density lipoprotein particle binding / negative regulation of focal adhesion assembly / Signaling by PDGF / negative regulation of plasminogen activation / platelet alpha granule / positive regulation of chemotaxis / negative regulation of cell migration involved in sprouting angiogenesis / fibrinogen binding / positive regulation of macrophage activation / transforming growth factor beta binding / sprouting angiogenesis / positive regulation of fibroblast migration / proteoglycan binding / negative regulation of cell-matrix adhesion / negative regulation of endothelial cell migration / negative regulation of receptor guanylyl cyclase signaling pathway / negative regulation of interleukin-10 production / Syndecan interactions / extracellular matrix structural constituent / phosphatidylserine binding / negative regulation of endothelial cell proliferation / positive regulation of transforming growth factor beta receptor signaling pathway / endopeptidase inhibitor activity / positive regulation of macrophage chemotaxis / behavioral response to pain / fibronectin binding / response to progesterone / response to testosterone / negative regulation of blood vessel endothelial cell migration / negative regulation of fibrinolysis / fibroblast growth factor binding / positive regulation of phosphorylation / response to glucose / negative regulation of tumor necrosis factor production / positive regulation of endothelial cell apoptotic process / positive regulation of blood vessel endothelial cell migration / response to magnesium ion / Integrin cell surface interactions / response to mechanical stimulus / nitric oxide-cGMP-mediated signaling / negative regulation of angiogenesis / laminin binding / positive regulation of endothelial cell migration / positive regulation of smooth muscle cell proliferation / secretory granule / response to endoplasmic reticulum stress / platelet alpha granule lumen / negative regulation of extrinsic apoptotic signaling pathway / cellular response to tumor necrosis factor / sarcoplasmic reticulum / positive regulation of translation / response to calcium ion / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / cellular response to growth factor stimulus / integrin binding / positive regulation of reactive oxygen species metabolic process / positive regulation of angiogenesis / positive regulation of tumor necrosis factor production / heparin binding / Platelet degranulation / cell migration / cellular response to heat / protease binding / extracellular matrix / response to hypoxia / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cell adhesion / positive regulation of MAPK cascade / inflammatory response / response to xenobiotic stimulus / positive regulation of cell migration / immune response / negative regulation of cell population proliferation / endoplasmic reticulum lumen / external side of plasma membrane / positive regulation of cell population proliferation / calcium ion binding / negative regulation of apoptotic process / cell surface / endoplasmic reticulum
Similarity search - Function
TSP-1 type 1 repeat / Thrombospondin type-1 (TSP1) repeat / Thrombospondin, C-terminal / Thrombospondin, type 3 repeat / Thrombospondin C-terminal region / Thrombospondin type-3 (TSP3) repeat profile. / Thrombospondin C-terminal domain profile. / Thrombospondin, type 3-like repeat / Thrombospondin type 3 repeat / TSP type-3 repeat ...TSP-1 type 1 repeat / Thrombospondin type-1 (TSP1) repeat / Thrombospondin, C-terminal / Thrombospondin, type 3 repeat / Thrombospondin C-terminal region / Thrombospondin type-3 (TSP3) repeat profile. / Thrombospondin C-terminal domain profile. / Thrombospondin, type 3-like repeat / Thrombospondin type 3 repeat / TSP type-3 repeat / : / Thrombospondin N-terminal -like domains. / von Willebrand factor type C domain / VWFC domain signature. / VWFC domain profile. / von Willebrand factor (vWF) type C domain / VWFC domain / Thrombospondin type 1 domain / Thrombospondin type-1 (TSP1) repeat superfamily / Thrombospondin type-1 (TSP1) repeat profile. / Thrombospondin type 1 repeats / Thrombospondin type-1 (TSP1) repeat / EGF-like calcium-binding domain / Calcium-binding EGF-like domain / Single Sheet / Epidermal growth factor-like domain. / EGF-like domain profile. / EGF-like domain signature 2. / EGF-like domain / Concanavalin A-like lectin/glucanase domain superfamily / Mainly Beta
Similarity search - Domain/homology
alpha-L-fucopyranose / beta-L-fucopyranose / Thrombospondin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å
AuthorsTan, K. / Duquette, M. / Liu, J. / Dong, Y. / Zhang, R. / Joachimiak, A. / Lawler, J. / Wang, J.-H.
CitationJournal: J.Cell Biol. / Year: 2002
Title: Crystal structure of the TSP-1 type 1 repeats: a novel layered fold and its biological implication.
Authors: Tan, K. / Duquette, M. / Liu, J.H. / Dong, Y. / Zhang, R. / Joachimiak, A. / Lawler, J. / Wang, J.H.
History
DepositionMay 17, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 18, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Structure summary
Category: chem_comp / database_PDB_caveat ...chem_comp / database_PDB_caveat / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Thrombospondin 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,5053
Polymers12,1771
Non-polymers3282
Water2,774154
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.63, 84.41, 37.17
Angle α, β, γ (deg.)90, 108.67, 90
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Thrombospondin 1


Mass: 12176.628 Da / Num. of mol.: 1 / Fragment: TSP Type 1 Repeats 2 and 3 (residues 434-546)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: THBS1 / Plasmid: PMT-BIP-V5-HIS A / Genus (production host): Drosophila / Cell (production host): S2 cells / Production host: Drosophila (fruit flies) / References: UniProt: P07996
#2: Sugar ChemComp-FUL / beta-L-fucopyranose / beta-L-fucose / 6-deoxy-beta-L-galactopyranose / L-fucose / fucose / 6-DEOXY-BETA-L-GALACTOSE


Type: L-saccharide, beta linking / Mass: 164.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O5
IdentifierTypeProgram
LFucpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-L-fucopyranoseCOMMON NAMEGMML 1.0
b-L-FucpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
FucSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Sugar ChemComp-FUC / alpha-L-fucopyranose / alpha-L-fucose / 6-deoxy-alpha-L-galactopyranose / L-fucose / fucose


Type: L-saccharide, alpha linking / Mass: 164.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O5
IdentifierTypeProgram
LFucpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-L-fucopyranoseCOMMON NAMEGMML 1.0
a-L-FucpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
FucSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 154 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 3.56 Å3/Da / Density % sol: 65.2 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.5 M sodium potassium tartrate and 0.1 M sodium acetate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails (eV)
10.5 Msodium potassium tartrate1reservoir
20.1 Msodium acetate1reservoirpH5.5

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 19-ID11.00803, 1.00808, 1.0596
SYNCHROTRONAPS 19-ID21.1
Detector
TypeIDDetectorDate
ADSC QUANTUM 41CCDDec 17, 2000
ADSC QUANTUM 42CCDDec 17, 2000
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1GraphiteMADMx-ray1
2GraphiteSINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.008031
21.008081
31.05961
41.11
ReflectionResolution: 1.9→20 Å / Num. obs: 15123 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Biso Wilson estimate: 26.4 Å2 / Rmerge(I) obs: 0.075 / Net I/σ(I): 14.6
Reflection shellResolution: 1.9→1.97 Å / Rmerge(I) obs: 0.469 / Mean I/σ(I) obs: 3.8 / % possible all: 99.7
Reflection
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 20 Å / Num. obs: 15485 / Num. measured all: 162978
Reflection shell
*PLUS
% possible obs: 99.7 %

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Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-2000data reduction
MLPHAREphasing
X-PLOR3.851refinement
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 1.9→20 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.282 1533 10 %Random
Rwork0.238 ---
all0.235 15123 --
obs0.235 15123 99.8 %-
Displacement parametersBiso mean: 42.28 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.345 Å0.321 Å
Luzzati d res low-3 Å
Luzzati sigma a0.345 Å0.321 Å
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms844 0 20 154 1018
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_angle_deg1.631
X-RAY DIFFRACTIONx_dihedral_angle_d27.854
X-RAY DIFFRACTIONx_improper_angle_d0.825
LS refinement shellResolution: 1.9→1.99 Å / Total num. of bins used: 8
RfactorNum. reflection
Rfree0.457 168
Rwork0.439 1545
obs-1545
Refinement
*PLUS
Lowest resolution: 20 Å / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg27.854
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.825

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