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- PDB-1z78: Crystal Structure of the Thrombospondin-1 N-terminal domain -

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Basic information

Entry
Database: PDB / ID: 1z78
TitleCrystal Structure of the Thrombospondin-1 N-terminal domain
ComponentsThrombospondin 1
KeywordsCELL ADHESION / TSP-1 / NTSP-1
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 / chronic inflammatory response / negative regulation of sprouting angiogenesis / negative regulation of endothelial cell chemotaxis / Defective B3GALTL causes PpS / positive regulation of extrinsic apoptotic signaling pathway via death domain receptors / 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 / chronic inflammatory response / negative regulation of sprouting angiogenesis / negative regulation of endothelial cell chemotaxis / Defective B3GALTL causes PpS / positive regulation of extrinsic apoptotic signaling pathway via death domain receptors / O-glycosylation of TSR domain-containing proteins / positive regulation of transforming growth factor beta1 production / 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 / engulfment of apoptotic cell / low-density lipoprotein particle binding / negative regulation of focal adhesion assembly / fibrinogen complex / peptide cross-linking / positive regulation of chemotaxis / fibrinogen binding / Signaling by PDGF / platelet alpha granule / negative regulation of interleukin-12 production / 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 endothelial cell apoptotic process / negative regulation of endothelial cell migration / positive regulation of fibroblast migration / sprouting angiogenesis / proteoglycan binding / extracellular matrix structural constituent / Syndecan interactions / endopeptidase inhibitor activity / negative regulation of cell-matrix adhesion / phosphatidylserine binding / positive regulation of macrophage chemotaxis / negative regulation of cGMP-mediated signaling / negative regulation of endothelial cell proliferation / response to testosterone / fibroblast growth factor binding / behavioral response to pain / positive regulation of transforming growth factor beta receptor signaling pathway / negative regulation of blood vessel endothelial cell migration / response to magnesium ion / fibronectin binding / response to unfolded protein / positive regulation of blood vessel endothelial cell migration / laminin binding / Integrin cell surface interactions / positive regulation of blood coagulation / negative regulation of fibrinolysis / response to glucose / response to mechanical stimulus / positive regulation of phosphorylation / extracellular matrix / response to endoplasmic reticulum stress / negative regulation of angiogenesis / positive regulation of endothelial cell migration / positive regulation of translation / platelet alpha granule lumen / response to progesterone / sarcoplasmic reticulum / secretory granule / negative regulation of extrinsic apoptotic signaling pathway / positive regulation of smooth muscle cell proliferation / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / positive regulation of MAP kinase activity / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / cellular response to growth factor stimulus / response to calcium ion / positive regulation of angiogenesis / positive regulation of reactive oxygen species metabolic process / cell migration / integrin binding / positive regulation of tumor necrosis factor production / Platelet degranulation / cellular response to heat / heparin binding / cellular response to tumor necrosis factor / collagen-containing extracellular matrix / protease binding / response to hypoxia / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cell adhesion / positive regulation of cell migration / immune response / response to xenobiotic stimulus / inflammatory response / endoplasmic reticulum lumen / negative regulation of cell population proliferation / external side of plasma membrane / apoptotic process / calcium ion binding / positive regulation of cell population proliferation / negative regulation of apoptotic process / cell surface / endoplasmic reticulum
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. / EGF domain / EGF domain / 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: 1.8 Å
AuthorsTan, K. / Wang, J. / Lawler, J.
CitationJournal: Structure / Year: 2006
Title: The structures of the thrombospondin-1 N-terminal domain and its complex with a synthetic pentameric heparin.
Authors: Tan, K. / Duquette, M. / Liu, J.H. / Zhang, R. / Joachimiak, A. / Wang, J.H. / Lawler, J.
History
DepositionMar 24, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 17, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 3, 2024Group: 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
Item: _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


Theoretical massNumber of molelcules
Total (without water)23,5991
Polymers23,5991
Non-polymers00
Water1,76598
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.812, 41.899, 53.458
Angle α, β, γ (deg.)90, 100.649, 90
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Thrombospondin 1 /


Mass: 23598.799 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-HisA / Production host: Drosophila melanogaster (fruit fly) / Strain (production host): Drosophila S2 Cells / References: UniProt: P07996
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 98 / Source method: isolated from a natural source / Formula: H2O

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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: 1.9 Å3/Da / Density % sol: 35.1 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 30% PEG1500 and 0.1 M NaAc, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.07218 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 31, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07218 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 17415 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.9 % / Biso Wilson estimate: 22.74 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 32.12
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.427 / Mean I/σ(I) obs: 2.75 / Num. unique all: 1672 / % possible all: 96.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-2000data reduction
AMoREphasing
CNS1.1refinement
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: NTSP-1 structure from NTSP-1/Arixtra complex to be deposited

Resolution: 1.8→30 Å / σ(F): 3 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.259 1472 9.4 %Random
Rwork0.236 ---
all0.253 17415 --
obs0.237 14668 84.23 %-
Displacement parametersBiso mean: 26.91 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.341 Å0.313 Å
Luzzati d res low-3 Å
Luzzati sigma a0.315 Å0.282 Å
Refinement stepCycle: LAST / Resolution: 1.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1594 0 0 101 1695
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0066
X-RAY DIFFRACTIONc_angle_deg1.63
X-RAY DIFFRACTIONc_dihedral_angle_d26.92
X-RAY DIFFRACTIONc_improper_angle_d1.39
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkRefine-IDNum. reflection obs
1.8-1.820.2834260.2714X-RAY DIFFRACTION201
1.82-1.840.379370.3646X-RAY DIFFRACTION495
1.84-1.870.2834190.2521X-RAY DIFFRACTION172

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