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- PDB-2ouj: The crystal structure of the Thrombospondin-1 N-terminal domain i... -

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Basic information

Entry
Database: PDB / ID: 2ouj
TitleThe crystal structure of the Thrombospondin-1 N-terminal domain in complex with fractionated Heparin DP8
ComponentsThrombospondin-1
KeywordsCELL ADHESION / TSP-1 / TSPN-1 / HBD / Fractionated Heparin / DP8
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 / negative regulation of dendritic cell antigen processing and presentation / negative regulation of nitric oxide mediated signal transduction / negative regulation of sprouting angiogenesis / chronic inflammatory response / negative regulation of endothelial cell chemotaxis / positive regulation of extrinsic apoptotic signaling pathway via death domain receptors / Defective B3GALTL causes PpS / O-glycosylation of TSR domain-containing proteins ...negative regulation of antigen processing and presentation of peptide or polysaccharide antigen via MHC class II / collagen V binding / negative regulation of dendritic cell antigen processing and presentation / negative regulation of nitric oxide mediated signal transduction / negative regulation of sprouting angiogenesis / chronic inflammatory response / negative regulation of endothelial cell chemotaxis / positive regulation of extrinsic apoptotic signaling pathway via death domain receptors / Defective B3GALTL causes PpS / O-glycosylation of TSR domain-containing proteins / negative regulation of fibroblast growth factor receptor signaling pathway / negative regulation of long-chain fatty acid import across plasma membrane / negative regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis / positive regulation of transforming growth factor beta1 production / engulfment of apoptotic cell / fibrinogen complex / negative regulation of focal adhesion assembly / low-density lipoprotein particle binding / Signaling by PDGF / platelet alpha granule / negative regulation of interleukin-12 production / positive regulation of chemotaxis / peptide cross-linking / fibrinogen binding / negative regulation of cell migration involved in sprouting angiogenesis / negative regulation of plasminogen activation / positive regulation of macrophage activation / transforming growth factor beta binding / positive regulation of fibroblast migration / sprouting angiogenesis / proteoglycan binding / negative regulation of endothelial cell migration / extracellular matrix structural constituent / endopeptidase inhibitor activity / negative regulation of cGMP-mediated signaling / Syndecan interactions / negative regulation of interleukin-10 production / positive regulation of macrophage chemotaxis / phosphatidylserine binding / positive regulation of transforming growth factor beta receptor signaling pathway / fibroblast growth factor binding / negative regulation of endothelial cell proliferation / response to testosterone / behavioral response to pain / response to magnesium ion / negative regulation of blood vessel endothelial cell migration / positive regulation of endothelial cell apoptotic process / fibronectin binding / negative regulation of tumor necrosis factor production / response to unfolded protein / positive regulation of blood vessel endothelial cell migration / negative regulation of cell-matrix adhesion / positive regulation of blood coagulation / negative regulation of fibrinolysis / Integrin cell surface interactions / response to glucose / positive regulation of phosphorylation / response to mechanical stimulus / nitric oxide-cGMP-mediated signaling / laminin binding / positive regulation of endothelial cell migration / response to endoplasmic reticulum stress / extracellular matrix / : / negative regulation of angiogenesis / platelet alpha granule lumen / secretory granule / sarcoplasmic reticulum / response to progesterone / positive regulation of MAP kinase activity / positive regulation of translation / negative regulation of extrinsic apoptotic signaling pathway / positive regulation of smooth muscle cell proliferation / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / cellular response to growth factor stimulus / response to calcium ion / positive regulation of angiogenesis / positive regulation of reactive oxygen species metabolic process / positive regulation of tumor necrosis factor production / cell migration / integrin binding / Platelet degranulation / cellular response to tumor necrosis factor / heparin binding / cellular response to heat / protease binding / collagen-containing extracellular matrix / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / response to hypoxia / cell adhesion / positive regulation of cell migration / immune response / inflammatory response / response to xenobiotic stimulus / endoplasmic reticulum lumen / external side of plasma membrane / negative regulation of cell population proliferation / positive regulation of cell population proliferation / calcium ion binding / negative regulation of apoptotic process
Similarity search - Function
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. ...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 / Epidermal growth factor-like domain. / Jelly Rolls - #200 / EGF-like domain profile. / EGF-like domain signature 2. / EGF-like domain / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsTan, K. / Joachimiak, A. / Wang, J. / Lawler, J.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: Heparin-induced cis- and trans-Dimerization Modes of the Thrombospondin-1 N-terminal Domain.
Authors: Tan, K. / Duquette, M. / Liu, J.H. / Shanmugasundaram, K. / Joachimiak, A. / Gallagher, J.T. / Rigby, A.C. / Wang, J.H. / Lawler, J.
History
DepositionFeb 11, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 8, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 30, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Thrombospondin-1


Theoretical massNumber of molelcules
Total (without water)27,5561
Polymers27,5561
Non-polymers00
Water70339
1
A: Thrombospondin-1

A: Thrombospondin-1


Theoretical massNumber of molelcules
Total (without water)55,1122
Polymers55,1122
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Unit cell
Length a, b, c (Å)95.497, 42.059, 52.965
Angle α, β, γ (deg.)90.00, 91.88, 90.00
Int Tables number5
Space group name H-MC121
DetailsTSPN-1 is a monomer by itself. In presence of DP8, it forms a symmetric heparin-linked dimer in the structure. The symmetry operator to generate the partner is (1-x,0,1-z). AUTHORS STATE THAT THE BIOLOGICAL UNIT OF THE TSPN-1 PROTEIN IS A MONOMER, HOWEVER, IN PRESENCE OF HEPARIN DP8, THE PROTEIN IS PROPOSED TO FORM A SYMMETRICAL, HEPARIN-LINKED, DIMER. SEE REMARK 350 FOR INFORMATION ON GENERATING OF THIS DIMER.

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Components

#1: Protein Thrombospondin-1


Mass: 27556.102 Da / Num. of mol.: 1 / Fragment: N-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: THBS1, TSP, TSP1 / Plasmid: PMT/BIP/V5-HIS A / Production host: Drosophila melanogaster (fruit fly) / Strain (production host): DROSOPHILA S2 CELL / References: UniProt: P07996
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 39 / 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: 1

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Sample preparation

CrystalDensity Matthews: 1.93 Å3/Da / Density % sol: 36.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 30% PEG1500, 0.08M Sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.0332 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 15, 2006 / Details: mirror
RadiationMonochromator: Si 111 Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 14441 / Num. obs: 14441 / % possible obs: 86.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.4 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 34.4
Reflection shellResolution: 1.9→1.99 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.406 / Mean I/σ(I) obs: 2.1 / Num. unique all: 881 / % possible all: 53.5

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Processing

Software
NameClassification
SBC-Collectdata collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1Z78

1z78


Resolution: 1.9→50 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: Fractionated heparin DP8 is chemically heterogeneous and disordered in the structure. Authors were able to see only uncharacterized densities around heparin binding sites of TSPN-1 and model ...Details: Fractionated heparin DP8 is chemically heterogeneous and disordered in the structure. Authors were able to see only uncharacterized densities around heparin binding sites of TSPN-1 and model some of them as water molecules.
RfactorNum. reflection% reflectionSelection details
Rfree0.276 1379 -Random
Rwork0.253 ---
all0.256 13515 --
obs0.256 13515 80.5 %-
Refinement stepCycle: LAST / Resolution: 1.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1579 0 0 39 1618
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_d0.0056
X-RAY DIFFRACTIONc_angle_deg1.592
LS refinement shellResolution: 1.9→1.95 Å /
RfactorNum. reflection
Rfree0.408 54
Rwork0.297 -
obs-512

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