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- PDB-1za4: Crystal Structure of the Thrombospondin-1 N-terminal Domain in Co... -

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Basic information

Entry
Database: PDB / ID: 1za4
TitleCrystal Structure of the Thrombospondin-1 N-terminal Domain in Complex with Arixtra
ComponentsThrombospondin 1
KeywordsCELL ADHESION / TSP-1 / NTSP-1 / HBD / ARIXTRA
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 / engulfment of apoptotic cell / Defective B3GALTL causes PpS ...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 / engulfment of apoptotic cell / 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 / fibrinogen complex / negative regulation of focal adhesion assembly / low-density lipoprotein particle binding / peptide cross-linking / Signaling by PDGF / platelet alpha granule / negative regulation of interleukin-12 production / fibrinogen binding / positive regulation of chemotaxis / 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 / proteoglycan binding / sprouting angiogenesis / 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 / phosphatidylserine binding / positive regulation of transforming growth factor beta receptor signaling pathway / positive regulation of macrophage chemotaxis / negative regulation of endothelial cell proliferation / fibroblast growth factor binding / response to testosterone / behavioral response to pain / response to magnesium ion / negative regulation of blood vessel endothelial cell migration / fibronectin binding / negative regulation of tumor necrosis factor production / positive regulation of endothelial cell apoptotic process / negative regulation of cell-matrix adhesion / positive regulation of blood vessel endothelial cell migration / positive regulation of blood coagulation / negative regulation of fibrinolysis / response to unfolded protein / Integrin cell surface interactions / positive regulation of phosphorylation / response to glucose / response to mechanical stimulus / nitric oxide-cGMP-mediated signaling / laminin binding / positive regulation of endothelial cell migration / positive regulation of MAP kinase activity / extracellular matrix / response to endoplasmic reticulum stress / negative regulation of angiogenesis / platelet alpha granule lumen / secretory granule / sarcoplasmic reticulum / response to progesterone / 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 / integrin binding / Platelet degranulation / cell migration / cellular response to tumor necrosis factor / heparin binding / cellular response to heat / protease binding / : / response to hypoxia / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cell adhesion / immune response / positive regulation of cell migration / inflammatory response / endoplasmic reticulum lumen / response to xenobiotic stimulus / external side of plasma membrane / negative regulation of cell population proliferation / apoptotic process / 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
Chem-SGN / Thrombospondin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å
AuthorsTan, K. / Wang, J.H. / 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
DepositionApr 5, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 24, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 6, 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
Remark 600HETEROGEN ARIXTRA (FONDAPARINUX SODIUM) IS A SYNTHETIC MODIFIED PENTAMERIC HEPARIN. THE COMPLETE ...HETEROGEN ARIXTRA (FONDAPARINUX SODIUM) IS A SYNTHETIC MODIFIED PENTAMERIC HEPARIN. THE COMPLETE ARIXTRA MOLECULE WAS NOT OBSERVED. SGN, N,O6-DISULFO-GLUCOSAMINE IS PART OF ARIXTRA MOLECULE (DEFINED AS FIFTH UNIT) AND SO4, SULFATE IONS ARE ALSO PART OF ARIXTRA MOLECULE (FRAGMENTS FROM THE REST OF THE UNITS).

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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)28,4707
Polymers27,6501
Non-polymers8206
Water1,40578
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.404, 53.053, 92.723
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Thrombospondin 1


Mass: 27649.893 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 / Genus (production host): Drosophila / Production host: Drosophila (fruit flies) / Strain (production host): Drosophila S2 cell / References: UniProt: P07996
#2: Sugar ChemComp-SGN / 2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose / N,O6-DISULFO-GLUCOSAMINE / 6-O-sulfo-N-sulfo-alpha-D-glucosamine / 2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucose / 2-deoxy-6-O-sulfo-2-(sulfoamino)-D-glucose / 2-deoxy-6-O-sulfo-2-(sulfoamino)-glucose


Type: D-saccharide, alpha linking / Mass: 339.298 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H13NO11S2
IdentifierTypeProgram
DGlcpNS[6S]aCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-sulfo-6-sulfo-a-D-glucopyranoseCOMMON NAMEGMML 1.0
a-D-GlcpNSO36SO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 78 / 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: 2 Å3/Da / Density % sol: 37.3 %
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

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 19-ID10.97923, 0.97928
SYNCHROTRONAPS 19-ID20.97923
Detector
TypeIDDetectorDate
ADSC QUANTUM 3151CCDOct 31, 2004
ADSC QUANTUM 3152CCDOct 31, 2004
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1GraphiteMADMx-ray1
2GraphiteSINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.979231
20.979281
ReflectionResolution: 1.9→50 Å / Num. obs: 30776 / % possible obs: 96.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Biso Wilson estimate: 28.7 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 27.1
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.359 / Mean I/σ(I) obs: 1.85 / Num. unique all: 2479 / % possible all: 78.2

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Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-2000data reduction
MLPHAREphasing
CNS1.1refinement
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 1.9→25 Å / σ(F): 3 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.275 2443 -Random
Rwork0.245 ---
all0.271 29639 --
obs0.253 24904 78.2 %-
Displacement parametersBiso mean: 34.2 Å2
Refine analyzeLuzzati coordinate error obs: 0.31 Å / Luzzati d res low obs: 3 Å / Luzzati sigma a obs: 0.15 Å
Refinement stepCycle: LAST / Resolution: 1.9→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1585 0 45 78 1708
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.43
X-RAY DIFFRACTIONc_dihedral_angle_d26.31
X-RAY DIFFRACTIONc_improper_angle_d1.25
LS refinement shellResolution: 1.9→1.97 Å
RfactorNum. reflection
Rfree0.259 115
Rwork0.256 -
obs-881

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