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- PDB-2cef: Phosphorylation of the Cytoplasmic Tail of Tissue Factor and its ... -

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Basic information

Entry
Database: PDB / ID: 2cef
TitlePhosphorylation of the Cytoplasmic Tail of Tissue Factor and its Role in Modulating Structure and Binding Affinity.
ComponentsTISSUE FACTOR
KeywordsBLOOD CLOTTING / COAGULATION PROTEIN / PIN1 / WW DOMAIN / BLOOD COAGULATION PROTEIN / LIPOPROTEIN / 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 / DYANA AMBER 8.0
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 6, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 13, 2007Provider: repository / Type: Initial release
Revision 1.1Dec 5, 2012Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Other / Structure summary / Version format compliance
Revision 1.2Jan 17, 2018Group: Structure summary / Category: struct / Item: _struct.title
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 2.1Nov 6, 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.pdbx_dist_value / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TISSUE FACTOR


Theoretical massNumber of molelcules
Total (without water)2,2231
Polymers2,2231
Non-polymers00
Water00
1


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

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Components

#1: Protein/peptide TISSUE FACTOR / TFCD / TF / COAGULATION FACTOR III / THROMBOPLASTIN / CD142 ANTIGEN / TFPP


Mass: 2223.276 Da / Num. of mol.: 1
Fragment: TISSUE FACTOR CYTOPLASMIC DOMAIN, RESIDUES 277-295
Source method: obtained synthetically / Details: SER253 AND SER258 ARE PHOSPHORYLATED / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: P13726
Has protein modificationY
Sequence detailsTHIS IS ONLY THE CYTOPLASMIC DOMAIN OF THE WHOLE TISSUE FACTOR

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111ROESY
121NOESY
131TOCSY
141IP-COSY
NMR detailsText: THE NMR STRUCTURE OF THE PHOSPHORYLATED PEPTIDE WAS DETERMINED USING HOMONUCLEAR 2D NMR SPECTROSCOPY METHODS.

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Sample preparation

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

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NMR measurement

NMR spectrometer
ManufacturerField strength (MHz)Spectrometer-ID
Bruker8001
Bruker6002

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Processing

NMR software
NameVersionDeveloperClassification
DYANA AMBER8PONDER,J.W.refinement
NMRPipestructure solution
NMRViewstructure solution
DYANAstructure solution
Amber8structure solution
MOLMOLstructure solution
RefinementMethod: DYANA AMBER 8.0 / 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 ...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

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