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- PDB-2es3: Crystal Structure of Thrombospondin-1 N-terminal Domain in P1 For... -

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Basic information

Entry
Database: PDB / ID: 2es3
TitleCrystal Structure of Thrombospondin-1 N-terminal Domain in P1 Form at 1.85A Resolution
ComponentsThrombospondin-1
KeywordsSUGAR BINDING PROTEIN / Thrombospondin-1 / TSP-1 / TSPN / HBD
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 / negative regulation of focal adhesion assembly / low-density lipoprotein particle binding / fibrinogen complex / peptide cross-linking / fibrinogen binding / Signaling by PDGF / positive regulation of chemotaxis / platelet alpha granule / negative regulation of interleukin-12 production / positive regulation of endothelial cell apoptotic process / negative regulation of cell migration involved in sprouting angiogenesis / negative regulation of plasminogen activation / transforming growth factor beta binding / positive regulation of macrophage activation / positive regulation of fibroblast migration / sprouting angiogenesis / proteoglycan binding / negative regulation of endothelial cell migration / extracellular matrix structural constituent / Syndecan interactions / endopeptidase inhibitor activity / negative regulation of cell-matrix adhesion / negative regulation of cGMP-mediated signaling / positive regulation of macrophage chemotaxis / response to testosterone / fibroblast growth factor binding / phosphatidylserine binding / positive regulation of transforming growth factor beta receptor signaling pathway / behavioral response to pain / negative regulation of endothelial cell proliferation / response to magnesium ion / fibronectin binding / negative regulation of blood vessel endothelial cell migration / response to unfolded protein / positive regulation of blood vessel endothelial cell migration / Integrin cell surface interactions / positive regulation of blood coagulation / negative regulation of fibrinolysis / response to glucose / response to mechanical stimulus / positive regulation of phosphorylation / laminin binding / nitric oxide-cGMP-mediated signaling / positive regulation of endothelial cell migration / response to endoplasmic reticulum stress / negative regulation of angiogenesis / extracellular matrix / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / platelet alpha granule lumen / sarcoplasmic reticulum / secretory granule / response to progesterone / positive regulation of translation / negative regulation of extrinsic apoptotic signaling pathway / positive regulation of smooth muscle cell proliferation / positive regulation of MAP kinase activity / 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 / cell migration / 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 / response to xenobiotic stimulus / inflammatory response / immune response / negative regulation of cell population proliferation / endoplasmic reticulum lumen / external side of plasma membrane / calcium ion binding / positive regulation of cell population proliferation / negative regulation of apoptotic process / apoptotic process / cell surface
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: 1.85 Å
AuthorsTan, K. / 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
DepositionOct 25, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 31, 2006Provider: repository / Type: Initial release
Revision 1.1Feb 12, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 999SEQUENCE THE SEQUENCE OF THE WHOLE CONSTRUCT IS LISTED HERE: ...SEQUENCE THE SEQUENCE OF THE WHOLE CONSTRUCT IS LISTED HERE: RSPWNRIPESGGDNSVFDIFELTGAARKGSGRRLVKGPDPSSPAFRIEDA NLIPPVPDDKFQDLVDAVRTEKGFLLLASLRQMKKTRGTLLALERKDHSG QVFSVVSNGKAGTLDLSLTVQGKQHVVSVEEALLATGQWKSITLFVQEDR AQLYIDCEKMENAELDVPIQSVFTRDLASIARLRIAKGGVNDNFQGVLQN VRFVFGTTPEDILRNKGCSSSTSVLLTLDNNVVNGSSPAIRTNTGHHHHHH THE PURIFIED PROTEIN WAS PROCESSED BY AN UNKNOWN PROTEASE AFTER CONCENTRATION AND RE-PURIFIED BEFORE CRYSTALLIZATION. THE EXACT N-TERMINAL OR C-TERMINAL SEQUENCES ARE NOT KNOWN. THE SEQRES REPRESENTS THE RESIDUES IN THE COORDINATES FOR CHAIN A.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Thrombospondin-1
B: Thrombospondin-1


Theoretical massNumber of molelcules
Total (without water)45,8022
Polymers45,8022
Non-polymers00
Water4,630257
1
A: Thrombospondin-1


Theoretical massNumber of molelcules
Total (without water)22,9011
Polymers22,9011
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Thrombospondin-1


Theoretical massNumber of molelcules
Total (without water)22,9011
Polymers22,9011
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.024, 41.709, 59.986
Angle α, β, γ (deg.)73.63, 89.59, 75.73
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Thrombospondin-1


Mass: 22901.035 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 / Cell line (production host): S2 CELL / 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.: 257 / 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: 2.03 Å3/Da / Density % sol: 39.34 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 30% PEG1500 and 0.1M Sodium Acetate, 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: 1.07812 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 1, 2004
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07812 Å / Relative weight: 1
ReflectionResolution: 1.85→30 Å / Num. all: 29466 / Num. obs: 29466 / % possible obs: 94 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.4 % / Biso Wilson estimate: 30.6 Å2 / Rmerge(I) obs: 0.051 / Net I/σ(I): 21.08
Reflection shellResolution: 1.85→1.95 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 2.91 / Num. unique all: 2388 / % possible all: 75.4

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB code: 1Z78

1z78


Resolution: 1.85→24.43 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.916 / SU B: 3.834 / SU ML: 0.118 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.18 / ESU R Free: 0.17 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2498 1471 5.1 %RANDOM
Rwork0.18668 ---
all0.1899 27640 --
obs0.18996 27640 94.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.688 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å2-0.11 Å2-0.01 Å2
2--0.11 Å20.03 Å2
3----0.09 Å2
Refinement stepCycle: LAST / Resolution: 1.85→24.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3214 0 0 257 3471
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0223262
X-RAY DIFFRACTIONr_angle_refined_deg1.8141.9734403
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9975415
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.15524.267150
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.04215586
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.7871528
X-RAY DIFFRACTIONr_chiral_restr0.1520.2506
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022446
X-RAY DIFFRACTIONr_nbd_refined0.2490.21538
X-RAY DIFFRACTIONr_nbtor_refined0.310.22217
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1840.2259
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2860.277
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2070.234
X-RAY DIFFRACTIONr_mcbond_it1.2691.52125
X-RAY DIFFRACTIONr_mcangle_it2.00823321
X-RAY DIFFRACTIONr_scbond_it3.25631251
X-RAY DIFFRACTIONr_scangle_it5.2074.51082
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.338 106 -
Rwork0.252 1702 -
obs--78.78 %

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