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- PDB-7yyk: Crystal structure of the O-fucosylated form of TSRs1-3 from the h... -

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Basic information

Entry
Database: PDB / ID: 7yyk
TitleCrystal structure of the O-fucosylated form of TSRs1-3 from the human thrombospondin 1
ComponentsThrombospondin-1
KeywordsCELL ADHESION / O-fucosylation / PoFUT2 / thrombospondin 1 / TSRs
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. / EGF-like domain profile. / EGF-like domain signature 2. / EGF-like domain / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
alpha-L-fucopyranose / Thrombospondin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsBerardinelli, S.J. / Eletsky, A. / Valero-Gonzalez, J. / Ito, A. / Manjunath, R. / Hurtado-Guerrero, R. / Prestegard, J.R. / Woods, R.J. / Haltiwanger, R.S.
Funding support Spain, 1items
OrganizationGrant numberCountry
Spanish Ministry of Economy and Competitiveness Spain
CitationJournal: J.Biol.Chem. / Year: 2022
Title: O-fucosylation stabilizes the TSR3 motif in thrombospondin-1 by interacting with nearby amino acids and protecting a disulfide bond.
Authors: Berardinelli, S.J. / Eletsky, A. / Valero-Gonzalez, J. / Ito, A. / Manjunath, R. / Hurtado-Guerrero, R. / Prestegard, J.H. / Woods, R.J. / Haltiwanger, R.S.
History
DepositionFeb 18, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 25, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 1, 2022Group: Database references / Category: citation
Item: _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jul 6, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.title / _citation_author.name
Revision 1.3Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Thrombospondin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,9544
Polymers18,5641
Non-polymers3903
Water37821
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, Monomeric by gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area520 Å2
ΔGint6 kcal/mol
Surface area8670 Å2
Unit cell
Length a, b, c (Å)66.153, 85.197, 62.121
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 / Glycoprotein G


Mass: 18563.570 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: THBS1, TSP, TSP1 / Production host: Escherichia coli (E. coli) / References: UniProt: P07996
#2: Sugar ChemComp-FUC / alpha-L-fucopyranose / alpha-L-fucose / 6-deoxy-alpha-L-galactopyranose / L-fucose / fucose


Type: L-saccharide, alpha linking / Mass: 164.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H12O5 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
LFucpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-L-fucopyranoseCOMMON NAMEGMML 1.0
a-L-FucpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
FucSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.36 Å3/Da / Density % sol: 47.83 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: PEG 8000, zinc acetate, buffer MES

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 22, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.6→20 Å / Num. obs: 5645 / % possible obs: 99.8 % / Redundancy: 8.3 % / CC1/2: 0.987 / Rmerge(I) obs: 0.197 / Net I/σ(I): 6.2
Reflection shellResolution: 2.6→2.74 Å / Rmerge(I) obs: 0.859 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 813 / CC1/2: 0.871

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1LSL

1lsl


Resolution: 2.6→20 Å / Cor.coef. Fo:Fc: 0.914 / Cor.coef. Fo:Fc free: 0.853 / SU B: 30.421 / SU ML: 0.313 / Cross valid method: THROUGHOUT / ESU R: 0.458 / ESU R Free: 0.339 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.31663 162 2.9 %RANDOM
Rwork0.24908 ---
obs0.25103 5466 99.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 70.644 Å2
Baniso -1Baniso -2Baniso -3
1--0.9 Å20 Å2-0 Å2
2---2.58 Å20 Å2
3---3.47 Å2
Refinement stepCycle: 1 / Resolution: 2.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms850 0 24 22 896
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.013913
X-RAY DIFFRACTIONr_bond_other_d0.0050.014803
X-RAY DIFFRACTIONr_angle_refined_deg1.7381.6841243
X-RAY DIFFRACTIONr_angle_other_deg1.3161.6261873
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.915115
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.13522.72744
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.02615139
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.727156
X-RAY DIFFRACTIONr_chiral_restr0.0690.2119
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021033
X-RAY DIFFRACTIONr_gen_planes_other0.0120.02203
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.2245.448457
X-RAY DIFFRACTIONr_mcbond_other3.2275.44456
X-RAY DIFFRACTIONr_mcangle_it5.2858.14570
X-RAY DIFFRACTIONr_mcangle_other5.288.148571
X-RAY DIFFRACTIONr_scbond_it2.9015.693454
X-RAY DIFFRACTIONr_scbond_other2.8985.695455
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.5798.399672
X-RAY DIFFRACTIONr_long_range_B_refined7.50764.4751034
X-RAY DIFFRACTIONr_long_range_B_other7.50464.4931035
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.668 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.351 11 -
Rwork0.36 396 -
obs--99.27 %
Refinement TLS params.Method: refined / Origin x: -1.3272 Å / Origin y: 18.9855 Å / Origin z: 14.3263 Å
111213212223313233
T0.0508 Å20.0671 Å2-0.0333 Å2-0.0893 Å2-0.0318 Å2--0.4231 Å2
L3.0191 °2-3.1692 °20.8601 °2-3.3582 °2-0.9685 °2--0.4406 °2
S-0.1052 Å °-0.1455 Å °-0.1045 Å °0.0868 Å °0.1244 Å °0.1436 Å °-0.0188 Å °-0.0327 Å °-0.0192 Å °

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