[English] 日本語
Yorodumi
- PDB-2cez: Phosphorylation of the Cytoplasmic Tail of Tissue Factor and its ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2cez
TitlePhosphorylation of the Cytoplasmic Tail of Tissue Factor and its Role in Modulating Structure and Binding Affinity
ComponentsTISSUE FACTOR
KeywordsBLOOD CLOTTING / TISSUE FACTOR / PIN1 / WW DOMAIN / BLOOD COAGULATION / GLYCOPROTEIN / LIPOPROTEIN / MEMBRANE / PALMITATE / TRANSMEMBRANE
Function / homology
Function and homology information


activation of plasma proteins involved in acute inflammatory response / activation of blood coagulation via clotting cascade / serine-type peptidase complex / positive regulation of platelet-derived growth factor receptor signaling pathway / NGF-stimulated transcription / cytokine receptor activity / positive regulation of positive chemotaxis / Extrinsic Pathway of Fibrin Clot Formation / positive regulation of endothelial cell apoptotic process / positive regulation of TOR signaling ...activation of plasma proteins involved in acute inflammatory response / activation of blood coagulation via clotting cascade / serine-type peptidase complex / positive regulation of platelet-derived growth factor receptor signaling pathway / NGF-stimulated transcription / cytokine receptor activity / positive regulation of positive chemotaxis / Extrinsic Pathway of Fibrin Clot Formation / positive regulation of endothelial cell apoptotic process / positive regulation of TOR signaling / positive regulation of endothelial cell proliferation / positive regulation of interleukin-8 production / phospholipid binding / protein processing / cytokine-mediated signaling pathway / positive regulation of angiogenesis / blood coagulation / : / protease binding / positive regulation of cell migration / external side of plasma membrane / positive regulation of gene expression / cell surface / extracellular space / membrane / plasma membrane
Similarity search - Function
Tissue factor / Tissue factor, conserved site / Tissue factor signature. / Interferon/interleukin receptor domain / Interferon-alpha/beta receptor, fibronectin type III / : / Tissue factor / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Biological speciesHOMO SAPIENS (human)
MethodSOLUTION NMR / simulated annealing
AuthorsSen, M. / Agrawal, S. / Craft, J.W. / Ruf, W. / Legge, G.B.
CitationJournal: Open Spectrosc J / Year: 2009
Title: Spectroscopic Characterization of Successive Phosphorylation of the Tissue Factor Cytoplasmic Region.
Authors: Sen, M. / Herzik, M. / Craft, J.W. / Creath, A.L. / Agrawal, S. / Ruf, W. / Legge, G.B.
History
DepositionFeb 13, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 20, 2007Provider: repository / Type: Initial release
Revision 1.1Dec 5, 2012Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Other / Structure summary / Version format compliance
Revision 1.2Jan 17, 2018Group: Database references / Category: citation / Item: _citation.journal_abbrev / _citation.page_last
Revision 2.0Oct 2, 2019Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Other
Category: atom_site / pdbx_database_status ...atom_site / pdbx_database_status / pdbx_nmr_software / struct_conn
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.label_atom_id / _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _struct_conn.pdbx_leaving_atom_flag
Revision 2.1Oct 9, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: TISSUE FACTOR


Theoretical massNumber of molelcules
Total (without water)2,1431
Polymers2,1431
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 50LOWEST POTENTIAL ENERGY ENSEMBLES
RepresentativeModel #1

-
Components

#1: Protein/peptide TISSUE FACTOR / TFSP 253 / TF / COAGULATION FACTOR III / THROMBOPLASTIN / CD142 ANTIGEN


Mass: 2143.297 Da / Num. of mol.: 1
Fragment: TISSUE FACTOR CYTOPLASMIC DOMAIN, RESIDUES 277-295
Source method: obtained synthetically
Details: THIS PEPTIDE IS PHOSPHORYLATED AT THE POSITION OF SER253
Source: (synth.) HOMO SAPIENS (human) / References: UniProt: P13726
Compound detailsINITIATES BLOOD COAGULATION BY FORMING A COMPLEX WITH CIRCULATING FACTOR VII OR VIIA
Has protein modificationY
Sequence detailsCYTOPLASMIC DOMAIN OF TISSUE FACTOR, WHICH IS PHOSPHORYLATED AT SER253

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111ROESY
121NOESY
131TOCSY
141IP-COSY
NMR detailsText: THE SINGLE 253 PHOSPHORYLATED TFCD PEPTIDE NMR STRUCTURES WERE CALCULATED USING 2D HOMONUCLEAR NMR SPECTROSCOPY METHODS.

-
Sample preparation

DetailsContents: 90% WATER 10% D2O
Sample conditionsIonic strength: 0 / pH: 6 / Pressure: 1.0 atm / Temperature: 285.0 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker OTHERBrukerOTHER8001
Bruker6002

-
Processing

NMR software
NameVersionDeveloperClassification
Amber8PONDER,J.W.refinement
NMRPipestructure solution
NMRViewstructure solution
DYANAstructure solution
Amber8structure solution
MOLMOLstructure solution
RefinementMethod: simulated annealing / Software ordinal: 1
Details: INITIAL NMR STRUCTURES WERE CALCULATED BY DYANA, WHICH INCLUDES MODIFIED SEP RESIDUE, PHOSPHORYLATED SER, CRAFT AND LEGGE, 2005, J.BIOL MOL.NMR. TOP10 ANNEALLED STRUCTURES THEN FURTHER MINIMIZED VIA AMBER 8.0.
NMR ensembleConformer selection criteria: LOWEST POTENTIAL ENERGY ENSEMBLES
Conformers calculated total number: 50 / Conformers submitted total number: 10

+
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