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- PDB-2ouh: Crystal structure of the Thrombospondin-1 N-terminal domain in co... -

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Basic information

Entry
Database: PDB / ID: 2ouh
TitleCrystal structure of the Thrombospondin-1 N-terminal domain in complex with fractionated Heparin DP10
ComponentsThrombospondin-1
KeywordsCELL ADHESION / TSP-1 / TSPN-1 / HBD / Fractionated Heparin / DP10
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 / peptide cross-linking / low-density lipoprotein particle binding / Signaling by PDGF / platelet alpha granule / positive regulation of chemotaxis / negative regulation of interleukin-12 production / negative regulation of plasminogen activation / fibrinogen binding / negative regulation of cell migration involved in sprouting angiogenesis / positive regulation of macrophage activation / transforming growth factor beta binding / sprouting angiogenesis / proteoglycan binding / negative regulation of endothelial cell migration / positive regulation of fibroblast migration / extracellular matrix structural constituent / endopeptidase inhibitor activity / negative regulation of receptor guanylyl cyclase signaling pathway / Syndecan interactions / phosphatidylserine binding / negative regulation of interleukin-10 production / positive regulation of macrophage chemotaxis / positive regulation of transforming growth factor beta receptor signaling pathway / response to testosterone / negative regulation of endothelial cell proliferation / fibroblast growth factor binding / behavioral response to pain / fibronectin binding / response to magnesium ion / negative regulation of blood vessel endothelial cell migration / positive regulation of phosphorylation / negative regulation of cell-matrix adhesion / positive regulation of endothelial cell apoptotic process / negative regulation of tumor necrosis factor production / positive regulation of blood coagulation / negative regulation of fibrinolysis / positive regulation of blood vessel endothelial cell migration / response to unfolded protein / Integrin cell surface interactions / response to mechanical stimulus / response to glucose / nitric oxide-cGMP-mediated signaling / laminin binding / extracellular matrix / positive regulation of smooth muscle cell proliferation / positive regulation of endothelial cell migration / response to progesterone / secretory granule / platelet alpha granule lumen / response to endoplasmic reticulum stress / positive regulation of translation / negative regulation of angiogenesis / sarcoplasmic reticulum / negative regulation of extrinsic apoptotic signaling pathway / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / response to calcium ion / 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 / cellular response to tumor necrosis factor / cell migration / Platelet degranulation / heparin binding / : / cellular response to heat / protease binding / response to hypoxia / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cell adhesion / positive regulation of MAPK cascade / immune response / positive regulation of cell migration / response to xenobiotic stimulus / endoplasmic reticulum lumen / inflammatory response / negative regulation of cell population proliferation / external side of plasma membrane / positive regulation of cell population proliferation / apoptotic process / 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: 2.4 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 ...Data collection / Database references / Derived calculations / 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 9, 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
B: Thrombospondin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,6898
Polymers55,1122
Non-polymers5766
Water1,56787
1
A: Thrombospondin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8444
Polymers27,5561
Non-polymers2883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Thrombospondin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8444
Polymers27,5561
Non-polymers2883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.316, 41.069, 241.779
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsTSPN-1 is a monomer by itself. In presence of DP10, it forms a heparin-linked dimer.

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Components

#1: Protein Thrombospondin-1


Mass: 27556.102 Da / Num. of mol.: 2 / 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: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 87 / 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: 1.82 Å3/Da / Density % sol: 32.24 %
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: 0.99187 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 2, 2004 / Details: Mirror
RadiationMonochromator: Si 111 Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99187 Å / Relative weight: 1
ReflectionResolution: 2.4→100 Å / Num. all: 14771 / Num. obs: 14771 / % possible obs: 88.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Rmerge(I) obs: 0.046 / Net I/σ(I): 29.87
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.268 / Mean I/σ(I) obs: 3.63 / Num. unique all: 1048 / % possible all: 65.9

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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: 2.4→100 Å / σ(F): 0 / σ(I): 0
Details: Fractionated heparin DP10 is chemically heterogeneous and partially disordered in the structure. Authors were able to identify only some SO4 groups from the heparin but not the heparin ...Details: Fractionated heparin DP10 is chemically heterogeneous and partially disordered in the structure. Authors were able to identify only some SO4 groups from the heparin but not the heparin backbone due to its possible mobility. Instead, there are several water molecules being positioned into some uncharacterized densities near heparin binding sites. These densities are likely from partially disordered heparin dp10, not necessarily from water molecules. Including of these waters in the model was just for the refinement purposes.
RfactorNum. reflection% reflection
Rfree0.296 1140 -
Rwork0.253 --
all0.257 14228 -
obs0.257 14228 85.9 %
Refinement stepCycle: LAST / Resolution: 2.4→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3146 0 30 87 3263
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_d0.007
X-RAY DIFFRACTIONc_angle_deg1.629
LS refinement shellResolution: 2.4→2.48 Å /
RfactorNum. reflection
Rfree0.369 57
Rwork0.327 -
obs-760

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