[English] 日本語
Yorodumi
- PDB-1ux6: Structure of a thrombospondin C-terminal fragment reveals a novel... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1ux6
TitleStructure of a thrombospondin C-terminal fragment reveals a novel calcium core in the type 3 repeats
ComponentsTHROMBOSPONDIN-1
KeywordsCELL ADHESION / EXTRACELLULAR MATRIX / CALCIUM BINDING / L-TYPE LECTIN / GLYCOPROTEIN / CALCIUM-BINDING / HEPARIN-BINDING / EGF-LIKE DOMAIN
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 / low-density lipoprotein particle binding / negative regulation of focal adhesion assembly / engulfment of apoptotic cell / fibrinogen complex / peptide cross-linking / fibrinogen binding / positive regulation of chemotaxis / Signaling by PDGF / 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 / positive regulation of transforming growth factor beta receptor signaling pathway / behavioral response to pain / phosphatidylserine binding / negative regulation of endothelial cell proliferation / response to magnesium ion / negative regulation of blood vessel endothelial cell migration / fibronectin binding / 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 / laminin binding / positive regulation of phosphorylation / nitric oxide-cGMP-mediated signaling / response to endoplasmic reticulum stress / positive regulation of endothelial cell migration / negative regulation of angiogenesis / extracellular matrix / platelet alpha granule lumen / secretory granule / sarcoplasmic reticulum / positive regulation of translation / response to progesterone / 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 / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / cellular response to growth factor stimulus / response to calcium ion / positive regulation of angiogenesis / positive regulation of tumor necrosis factor production / positive regulation of reactive oxygen species metabolic process / cell migration / integrin binding / Platelet degranulation / cellular response to tumor necrosis factor / heparin binding / cellular response to heat / collagen-containing extracellular matrix / protease binding / 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 / apoptotic process / calcium ion binding / positive regulation of cell population proliferation / negative regulation of apoptotic process / cell surface
Similarity search - Function
TSP type-3 repeat / TSP type-3 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 type-3 repeat / TSP type-3 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. / 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 / Few Secondary Structures / Irregular / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 1.9 Å
AuthorsKvansakul, M. / Adams, J.C. / Hohenester, E.
CitationJournal: Embo J. / Year: 2004
Title: Structure of a Thrombospondin C-Terminal Fragment Reveals a Novel Calcium Core in the Type 3 Repeats
Authors: Kvansakul, M. / Adams, J.C. / Hohenester, E.
History
DepositionFeb 19, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 18, 2004Provider: repository / Type: Initial release
Revision 1.1May 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 12, 2017Group: Derived calculations / Category: pdbx_struct_conn_angle / struct_conn
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: THROMBOSPONDIN-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,36217
Polymers39,7211
Non-polymers64116
Water4,720262
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)162.340, 162.340, 85.140
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-2341-

HOH

21A-2359-

HOH

-
Components

#1: Protein THROMBOSPONDIN-1


Mass: 39721.078 Da / Num. of mol.: 1 / Fragment: RESIDUES 831-1170 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): 293-EBNA / Production host: HOMO SAPIENS (human) / References: UniProt: P07996
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 262 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED MUTATION A 992 CYS TO SER ENGINEERED MUTATION A 1067 ASN TO LYS ADHESIVE GLYCOPROTEIN ...ENGINEERED MUTATION A 992 CYS TO SER ENGINEERED MUTATION A 1067 ASN TO LYS ADHESIVE GLYCOPROTEIN MEDIATES CELL-CELL AND CELL-MATRIX INTERACTIONS. BINDS TO FIBRINOGEN, FIBRONECTIN, LAMININ, TYPE V COLLAGEN AND INTEGRINS ALPHA-V/BETA-1, ALPHA- V/BETA-3 AND ALPHA-IIB/BETA-3.

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.72 Å3/Da / Density % sol: 54 %
Crystal growpH: 7.5 / Details: pH 7.50
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
16-10 mg/mlprotein1drop
260 %MPD1reservoir
3100 mMHEPES1reservoirpH7.5
45 mM1reservoirCaAc2

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87
DetectorType: ADSC CCD / Detector: CCD / Date: Sep 15, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. obs: 32099 / % possible obs: 95.3 % / Redundancy: 5.4 % / Rmerge(I) obs: 0.086
Reflection shellResolution: 1.9→2 Å / Redundancy: 4 % / Rmerge(I) obs: 0.37 / % possible all: 92.9
Reflection
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 20 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.086
Reflection shell
*PLUS
% possible obs: 92.9 % / Redundancy: 4 % / Rmerge(I) obs: 0.37

-
Processing

Software
NameVersionClassification
CNS1.1refinement
MOSFLMdata reduction
SCALAdata scaling
MLPHAREphasing
RefinementMethod to determine structure: MIRAS / Resolution: 1.9→20 Å / Data cutoff high absF: 100000 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.227 3197 10 %RANDOM
Rwork0.199 ---
obs0.199 28902 95.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 58 Å2 / ksol: 0.366 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.18 Å2-2.14 Å20 Å2
2---2.18 Å20 Å2
3---4.36 Å2
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2667 0 16 262 2945
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.161.5
X-RAY DIFFRACTIONc_mcangle_it1.872
X-RAY DIFFRACTIONc_scbond_it1.762
X-RAY DIFFRACTIONc_scangle_it2.722.5
LS refinement shellResolution: 1.9→1.91 Å / Total num. of bins used: 50 /
RfactorNum. reflection
Rfree0.313 60
Rwork0.279 569
Refinement
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 20 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more