[English] 日本語
Yorodumi
- PDB-2ouh: Crystal structure of the Thrombospondin-1 N-terminal domain in co... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2ouh
TitleCrystal structure of the Thrombospondin-1 N-terminal domain in complex with fractionated Heparin DP10
ComponentsThrombospondin-1
KeywordsCELL ADHESION / TSP-1 / TSPN-1 / HBD / Fractionated Heparin / DP10
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 / thrombospondin complex / endothelial cell-cell adhesion / negative regulation of dendritic cell antigen processing and presentation / positive regulation of extrinsic apoptotic signaling pathway via death domain receptors / negative regulation of sprouting angiogenesis / chronic inflammatory response / negative regulation of endothelial cell chemotaxis / Defective B3GALTL causes PpS ...negative regulation of antigen processing and presentation of peptide or polysaccharide antigen via MHC class II / collagen V binding / thrombospondin complex / endothelial cell-cell adhesion / negative regulation of dendritic cell antigen processing and presentation / positive regulation of extrinsic apoptotic signaling pathway via death domain receptors / negative regulation of sprouting angiogenesis / chronic inflammatory response / negative regulation of endothelial cell chemotaxis / Defective B3GALTL causes PpS / negative regulation of fibroblast growth factor receptor signaling pathway / O-glycosylation of TSR domain-containing proteins / negative regulation of nitric oxide-cGMP mediated signal transduction / negative regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis / negative regulation of long-chain fatty acid import across plasma membrane / positive regulation of transforming growth factor beta1 production / fibrinogen complex / negative regulation of interleukin-12 production / blood coagulation, fibrin clot formation / engulfment of apoptotic cell / low-density lipoprotein particle binding / negative regulation of focal adhesion assembly / Signaling by PDGF / negative regulation of plasminogen activation / platelet alpha granule / positive regulation of chemotaxis / negative regulation of cell migration involved in sprouting angiogenesis / fibrinogen binding / positive regulation of macrophage activation / transforming growth factor beta binding / sprouting angiogenesis / positive regulation of fibroblast migration / proteoglycan binding / negative regulation of cell-matrix adhesion / negative regulation of endothelial cell migration / negative regulation of receptor guanylyl cyclase signaling pathway / negative regulation of interleukin-10 production / Syndecan interactions / extracellular matrix structural constituent / phosphatidylserine binding / negative regulation of endothelial cell proliferation / positive regulation of transforming growth factor beta receptor signaling pathway / endopeptidase inhibitor activity / positive regulation of macrophage chemotaxis / behavioral response to pain / fibronectin binding / response to progesterone / response to testosterone / negative regulation of blood vessel endothelial cell migration / negative regulation of fibrinolysis / fibroblast growth factor binding / positive regulation of phosphorylation / response to glucose / negative regulation of tumor necrosis factor production / positive regulation of endothelial cell apoptotic process / positive regulation of blood vessel endothelial cell migration / response to magnesium ion / Integrin cell surface interactions / response to mechanical stimulus / nitric oxide-cGMP-mediated signaling / negative regulation of angiogenesis / laminin binding / positive regulation of endothelial cell migration / positive regulation of smooth muscle cell proliferation / secretory granule / response to endoplasmic reticulum stress / platelet alpha granule lumen / negative regulation of extrinsic apoptotic signaling pathway / cellular response to tumor necrosis factor / sarcoplasmic reticulum / positive regulation of translation / response to calcium ion / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / cellular response to growth factor stimulus / integrin binding / positive regulation of reactive oxygen species metabolic process / positive regulation of angiogenesis / positive regulation of tumor necrosis factor production / heparin binding / Platelet degranulation / cell migration / cellular response to heat / protease binding / extracellular matrix / response to hypoxia / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cell adhesion / positive regulation of MAPK cascade / inflammatory response / response to xenobiotic stimulus / positive regulation of cell migration / immune response / negative regulation of cell population proliferation / endoplasmic reticulum lumen / external side of plasma membrane / positive regulation of cell population proliferation / calcium ion binding / negative regulation of apoptotic process / cell surface / endoplasmic reticulum
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 / Jelly Rolls - #200 / Epidermal growth factor-like domain. / 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: 2.4 Å
AuthorsTan, K. / Joachimiak, A. / 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
DepositionFeb 11, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 8, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 30, 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 1.3Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)55,6898
Polymers55,1122
Non-polymers5766
Water1,56787
1
A: Thrombospondin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8444
Polymers27,5561
Non-polymers2883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Thrombospondin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8444
Polymers27,5561
Non-polymers2883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.316, 41.069, 241.779
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsTSPN-1 is a monomer by itself. In presence of DP10, it forms a heparin-linked dimer.

-
Components

#1: Protein Thrombospondin-1


Mass: 27556.102 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 / Production host: Drosophila melanogaster (fruit fly) / Strain (production host): DROSOPHILA S2 CELL / References: UniProt: P07996
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 87 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.82 Å3/Da / Density % sol: 32.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 30% PEG1500, 0.08M Sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.99187 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 2, 2004 / Details: Mirror
RadiationMonochromator: Si 111 Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99187 Å / Relative weight: 1
ReflectionResolution: 2.4→100 Å / Num. all: 14771 / Num. obs: 14771 / % possible obs: 88.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Rmerge(I) obs: 0.046 / Net I/σ(I): 29.87
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.268 / Mean I/σ(I) obs: 3.63 / Num. unique all: 1048 / % possible all: 65.9

-
Processing

Software
NameClassification
SBC-Collectdata collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1Z78

1z78


Resolution: 2.4→100 Å / σ(F): 0 / σ(I): 0
Details: Fractionated heparin DP10 is chemically heterogeneous and partially disordered in the structure. Authors were able to identify only some SO4 groups from the heparin but not the heparin ...Details: Fractionated heparin DP10 is chemically heterogeneous and partially disordered in the structure. Authors were able to identify only some SO4 groups from the heparin but not the heparin backbone due to its possible mobility. Instead, there are several water molecules being positioned into some uncharacterized densities near heparin binding sites. These densities are likely from partially disordered heparin dp10, not necessarily from water molecules. Including of these waters in the model was just for the refinement purposes.
RfactorNum. reflection% reflection
Rfree0.296 1140 -
Rwork0.253 --
all0.257 14228 -
obs0.257 14228 85.9 %
Refinement stepCycle: LAST / Resolution: 2.4→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3146 0 30 87 3263
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_d0.007
X-RAY DIFFRACTIONc_angle_deg1.629
LS refinement shellResolution: 2.4→2.48 Å /
RfactorNum. reflection
Rfree0.369 57
Rwork0.327 -
obs-760

+
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://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