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- PDB-3r6b: Crystal Structure of Thrombospondin-1 TSR Domains 2 and 3 -

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Basic information

Entry
Database: PDB / ID: 3r6b
TitleCrystal Structure of Thrombospondin-1 TSR Domains 2 and 3
ComponentsThrombospondin-1
KeywordsCELL ADHESION / Disulfide bond / EGF-like domain / TSP-1 type 1 Repeat
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
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 / Epidermal growth factor-like domain. / Single Sheet / 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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsPage, R.C. / Klenotic, P.A. / Misra, S. / Silverstein, R.L.
CitationJournal: Protein Expr.Purif. / Year: 2011
Title: Expression, purification and structural characterization of functionally replete thrombospondin-1 type 1 repeats in a bacterial expression system.
Authors: Klenotic, P.A. / Page, R.C. / Misra, S. / Silverstein, R.L.
History
DepositionMar 21, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 10, 2011Provider: repository / Type: Initial release
Revision 1.1Aug 17, 2011Group: Database references
Revision 1.2Nov 16, 2011Group: Database references
Revision 1.3Sep 13, 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 1.4Nov 20, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,2909
Polymers16,7941
Non-polymers4978
Water1,69394
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)66.364, 84.817, 60.707
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Thrombospondin-1


Mass: 16793.723 Da / Num. of mol.: 1 / Fragment: UNP residues 434-547
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: THBS1, TSP, TSP1 / Plasmid: pGST parallel 1 / Production host: Escherichia coli (E. coli) / References: UniProt: P07996
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 94 / 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: 2.54 Å3/Da / Density % sol: 51.64 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 0.9M sodium potassium phosphate, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Mar 15, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→30.354 Å / Num. all: 6564 / Num. obs: 6564 / % possible obs: 94 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.8 % / Biso Wilson estimate: 39.6 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 16.6
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 3.84 % / Rmerge(I) obs: 0.227 / Mean I/σ(I) obs: 4.7 / Num. unique all: 691 / % possible all: 87.6

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Processing

Software
NameVersionClassification
StructureStudiodata collection
PHENIX(phenix.refine: 1.7_650)model building
PHENIX(phenix.refine: 1.7_650)refinement
d*TREKdata reduction
d*TREKdata scaling
PHENIX1.7_650phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1LSL

1lsl


Resolution: 2.4→30.354 Å / SU ML: 0.39 / σ(F): 0 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.2729 653 10.02 %RANDOM
Rwork0.2348 ---
all0.2387 6519 --
obs0.2387 6519 93.32 %-
Solvent computationShrinkage radii: 0.61 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 58.094 Å2 / ksol: 0.354 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--5.4604 Å2-0 Å20 Å2
2---3.2501 Å20 Å2
3---8.7105 Å2
Refinement stepCycle: LAST / Resolution: 2.4→30.354 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms855 0 32 94 981
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008916
X-RAY DIFFRACTIONf_angle_d1.2861209
X-RAY DIFFRACTIONf_dihedral_angle_d13.171330
X-RAY DIFFRACTIONf_chiral_restr0.088119
X-RAY DIFFRACTIONf_plane_restr0.006161
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4002-2.58540.37811250.32411109X-RAY DIFFRACTION90
2.5854-2.84540.3811300.29111169X-RAY DIFFRACTION95
2.8454-3.25680.30821290.24661164X-RAY DIFFRACTION94
3.2568-4.10160.25071270.2271151X-RAY DIFFRACTION92
4.1016-30.35590.22861420.20241273X-RAY DIFFRACTION97
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.2391-0.15870.00560.106-0.00560.0022-0.21-0.0548-0.19070.0042-0.11730.03650.2295-0.3345-0.0960.4918-0.11690.04270.2435-0.12350.2912-23.021-10.5834-24.6556
20.14510.09670.04640.352-0.15250.10550.0761-0.1098-0.1413-0.170.13750.04350.2257-0.03230.23950.2778-0.3251-0.129-0.0530.14490.3483-13.10239.4181-13.5351
31.12890.1310.71773.29642.33612.6046-0.24750.09370.08210.0267-0.31730.2751-0.60980.4376-0.10830.506-0.0944-0.01450.2463-0.01380.2445-16.53512.788-19.0645
40.3511-0.4117-0.51860.57310.59340.7634-0.0660.3879-0.5880.28330.10870.40570.4637-0.05260.10070.33630.00860.04320.2063-0.10380.4489-19.8946-13.9251-23.6273
51.1514-0.04170.28060.7349-0.59030.53380.01070.7232-0.3833-0.2373-0.40280.1545-0.36030.11630.1970.94530.01160.17170.5901-0.14070.3781-19.9091-15.9873-32.6103
60.1528-0.144-0.10960.15430.13050.1179-0.12660.01420.0303-0.0479-0.0489-0.1691-0.11510.1328-0.21130.7949-0.3084-0.02960.42290.32540.3859-16.92672.5313-23.994
70.85650.2692-0.02161.98730.6441.78240.1244-0.0428-0.068-0.21190.22090.17060.2029-0.02780.03990.2439-0.1997-0.19160.45340.14460.755-13.213918.1956-13.9244
85.75073.0514-1.06791.9307-0.77520.67170.09750.6041-0.2930.15390.0594-0.2198-0.2641-0.0027-0.04960.2873-0.0201-0.04550.23930.00780.305512.424433.4341-10.7244
90.30560.25970.07710.24970.13360.195-0.1663-0.0058-0.0139-0.0301-0.07820.012-0.09450.0323-0.27940.3211-0.1695-0.16480.41960.04761.047231.932349.9219-5.9953
101.161.0490.26711.36190.56010.31670.0411-0.0108-0.07070.1280.08540.0318-0.05060.05250.00490.2864-0.148-0.10480.43950.05140.322925.560343.0904-5.3973
111.48380.83290.09370.70910.02470.00330.05150.0073-0.25930.0617-0.3130.19410.2311-0.2701-1.23690.0905-0.097-0.1090.2189-0.02850.40295.040432.2961-10.0954
120.19190.0512-0.24740.42210.41980.86280.2893-0.3744-0.45630.3815-0.1297-0.20.33780.1344-0.09890.3986-0.1029-0.16310.3790.12510.382917.716535.1047-3.7926
130.0891-0.2507-0.07330.71020.18760.2605-0.09020.1938-0.28810.1165-0.15270.278-0.10910.05580.0150.3444-0.2607-0.10080.80810.19240.635140.051347.723-4.4711
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 415:423)
2X-RAY DIFFRACTION2(chain A and resid 424:435)
3X-RAY DIFFRACTION3(chain A and resid 436:442)
4X-RAY DIFFRACTION4(chain A and resid 443:449)
5X-RAY DIFFRACTION5(chain A and resid 450:457)
6X-RAY DIFFRACTION6(chain A and resid 458:464)
7X-RAY DIFFRACTION7(chain A and resid 465:470)
8X-RAY DIFFRACTION8(chain A and resid 471:484)
9X-RAY DIFFRACTION9(chain A and resid 485:491)
10X-RAY DIFFRACTION10(chain A and resid 492:497)
11X-RAY DIFFRACTION11(chain A and resid 498:510)
12X-RAY DIFFRACTION12(chain A and resid 511:523)
13X-RAY DIFFRACTION13(chain A and resid 524:529)

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