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- PDB-1boy: EXTRACELLULAR REGION OF HUMAN TISSUE FACTOR -

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Basic information

Entry
Database: PDB / ID: 1boy
TitleEXTRACELLULAR REGION OF HUMAN TISSUE FACTOR
ComponentsHUMAN TISSUE FACTOR
KeywordsCLASS 2 CYTOKINE RECEPTOR / INITIATOR OF BLOOD COAGULATION IN VERTEBRATES / COFACTOR FOR FACTOR VIIA / GLYCOPROTEIN / BLOOD COAGULATION
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 ...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 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.2 Å
AuthorsBoys, C.W.G. / Tuddenham, E.G.D. / Harlos, K.
Citation
Journal: Nature / Year: 1994
Title: Crystal structure of the extracellular region of human tissue factor.
Authors: Harlos, K. / Martin, D.M. / O'Brien, D.P. / Jones, E.Y. / Stuart, D.I. / Polikarpov, I. / Miller, A. / Tuddenham, E.G. / Boys, C.W.
#1: Journal: J.Mol.Biol. / Year: 1993
Title: Crystallization and Preliminary X-Ray Analysis of Human Tissue Factor Extracellular Domain
Authors: Boys, C.W. / Miller, A. / Harlos, K. / Martin, D.M. / Tuddenham, E.G. / O'Brien, D.P.
History
DepositionJan 11, 1996Processing site: BNL
Revision 1.0Jun 10, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HUMAN TISSUE FACTOR


Theoretical massNumber of molelcules
Total (without water)24,8271
Polymers24,8271
Non-polymers00
Water1,982110
1
A: HUMAN TISSUE FACTOR

A: HUMAN TISSUE FACTOR


Theoretical massNumber of molelcules
Total (without water)49,6532
Polymers49,6532
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Unit cell
Length a, b, c (Å)45.400, 45.400, 230.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein HUMAN TISSUE FACTOR / TF


Mass: 24826.512 Da / Num. of mol.: 1 / Fragment: EXTRACELLULAR DOMAIN, RESIDUES 1 - 219
Source method: isolated from a genetically manipulated source
Details: TYPE B CRYSTALS / Source: (gene. exp.) Homo sapiens (human) / Strain: W3110
Description: PURIFIED BY MONOCLONAL ANTIBODY AFFINITY, REVERSED PHASE HPLC AND ISO-ELECTRIC FOCUSSING
Gene: HUMAN TISSUE FACTOR CDNA CODON / Organ: BLOOD / Variant: TONA / Plasmid: PHGH4L (GENE 55:189-196, 1987)
Gene (production host): HUMAN TISSUE FACTOR CDNA CODONS 1-119
Production host: PERIPLASMIC SECRETION (U.S PAT 4963,495) / References: UniProt: P13726
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 110 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.39 Å3/Da / Density % sol: 48 %
Description: THE REDUNDANCY GIVEN ABOVE IS TO 2.2 ANGSTROMS RESOLUTION.
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
15.0 mg/mlprotein1drop
20.1 MHEPES1reservoir
32.6 Mammonium sulfate1reservoir

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 0.97
DetectorType: FUJI / Detector: IMAGE PLATE / Date: Mar 1, 1994
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionNum. obs: 12666 / % possible obs: 96 % / Observed criterion σ(I): 3 / Redundancy: 6.4 % / Rmerge(I) obs: 0.065
Reflection
*PLUS
Highest resolution: 2.2 Å

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Processing

Software
NameVersionClassification
DENZO/ SCALEPACKdata reduction
X-PLORrefinement
SCALEPACKdata scaling
RefinementResolution: 2.2→15 Å /
RfactorNum. reflection
Rwork0.203 -
obs0.203 12623
Refinement stepCycle: LAST / Resolution: 2.2→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1685 0 0 110 1795
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.014
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.98
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 48.9 Å2

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