[English] 日本語
Yorodumi
- PDB-1tfh: EXTRACELLULAR DOMAIN OF HUMAN TISSUE FACTOR -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1tfh
TitleEXTRACELLULAR DOMAIN OF HUMAN TISSUE FACTOR
ComponentsHUMAN TISSUE FACTOR
KeywordsCOAGULATION FACTOR / BLOOD COAGULATION / TISSUE FACTOR / GLYCOPROTEIN
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 / positive regulation of positive chemotaxis / Extrinsic Pathway of Fibrin Clot Formation / cytokine receptor activity / positive regulation of TOR signaling / positive regulation of endothelial cell proliferation ...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 / positive regulation of positive chemotaxis / Extrinsic Pathway of Fibrin Clot Formation / cytokine receptor activity / positive regulation of TOR signaling / positive regulation of endothelial cell proliferation / positive regulation of interleukin-8 production / protein processing / phospholipid binding / : / cytokine-mediated signaling pathway / positive regulation of angiogenesis / blood coagulation / protease binding / collagen-containing extracellular matrix / 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 / Immunoglobulins ...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 / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MIR, MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsHuang, M. / Syed, R. / Stura, E.A. / Stone, M.J. / Stefanko, R.S. / Ruf, W. / Edgington, T.S. / Wilson, I.A.
CitationJournal: J.Mol.Biol. / Year: 1998
Title: The mechanism of an inhibitory antibody on TF-initiated blood coagulation revealed by the crystal structures of human tissue factor, Fab 5G9 and TF.G9 complex.
Authors: Huang, M. / Syed, R. / Stura, E.A. / Stone, M.J. / Stefanko, R.S. / Ruf, W. / Edgington, T.S. / Wilson, I.A.
History
DepositionApr 10, 1997Processing site: BNL
Revision 1.0Feb 25, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 11, 2019Group: Database references / Derived calculations
Category: citation / pdbx_struct_assembly / pdbx_struct_assembly_gen
Item: _citation.title
Revision 1.4Aug 9, 2023Group: Database references / Refinement description / Category: database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Oct 16, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: HUMAN TISSUE FACTOR
B: HUMAN TISSUE FACTOR


Theoretical massNumber of molelcules
Total (without water)49,6532
Polymers49,6532
Non-polymers00
Water25214
1
A: HUMAN TISSUE FACTOR


Theoretical massNumber of molelcules
Total (without water)24,8271
Polymers24,8271
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: HUMAN TISSUE FACTOR


Theoretical massNumber of molelcules
Total (without water)24,8271
Polymers24,8271
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)64.393, 85.828, 112.901
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
/ NCS ensembles :
ID
1
2

NCS oper: (Code: given
Matrix: (-0.011162, -0.309875, -0.950712), (0.252914, 0.918981, -0.302503), (0.967424, -0.243825, 0.068114)
Vector: 101.78719, -2.7234, -11.94945)
DetailsTHE ASYMMETRIC UNIT CONTAINS TWO TISSUE FACTOR MOLECULES WITH CHAIN IDS OF A AND B. 14 WATER MOLECULES WERE IDENTIFIED AROUND MOLECULE A. MOLECULE B HAS ONLY A FEW CONTACTS (10 LESS THAN 5.0 ANGSTROMS) WITH ITS SYMMETRY-RELATED MOLECULES AND THUS HAS A MUCH HIGHER OVERALL B VALUE THAN MOLECULE A, WHICH HAS EXTENSIVE CONTACTS WITH ITS NEIGHBORING MOLECULES.

-
Components

#1: Protein HUMAN TISSUE FACTOR / TF / THROMBOPLASTIN / COAGULATION FACTOR III


Mass: 24826.512 Da / Num. of mol.: 2 / Fragment: EXTRACELLULAR DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line: BL21 / Gene: HUMAN TISSUE FACTOR EXTRACELLU / Organ: BLOOD / Plasmid: PTRCHISC (INVITROGEN) / Species (production host): Escherichia coli / Cellular location (production host): INCLUSION BODIES
Gene (production host): HUMAN TISSUE FACTOR EXTRACELLULAR DOMAIN
Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P13726
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / 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: 2.9 Å3/Da / Density % sol: 55 %
Crystal growTemperature: 278 K / pH: 7
Details: CRYSTAL CAN BE GROWN FROM 20MM PHOSPHATE BUFFER, PH 6.5, AT A 40MG/ML PROTEIN CONCENTRATION. THE CRYSTALS USED FOR DIFFRACTION STUDIES WERE IN FACT CRYSTALLIZED UNEXPECTEDLY IN 2 DAYS IN AN ...Details: CRYSTAL CAN BE GROWN FROM 20MM PHOSPHATE BUFFER, PH 6.5, AT A 40MG/ML PROTEIN CONCENTRATION. THE CRYSTALS USED FOR DIFFRACTION STUDIES WERE IN FACT CRYSTALLIZED UNEXPECTEDLY IN 2 DAYS IN AN NMR TUBE CONTAINING A SOLUTION OF APPROXIMATELY 3.5MM OF UNIFORMLY 15N-ENRICHED (~99 ATOM%) TISSUE FACTOR (AT ~85 MG/ML) IN 20MM KNA2PO4, 0.02%NAN3, 10% D2O AND 90% H2O, PH 7.0 AT 5 DEGREE., temperature 278K
Crystal grow
*PLUS
pH: 6.5 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 mMphosphate11
240 mg/mlprotein11

-
Data collection

DiffractionMean temperature: 297 K
Diffraction sourceSource: ROTATING ANODE / Type: ELLIOTT GX-18 / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Dec 1, 1994 / Details: COLLIMATOR
RadiationMonochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.27→19 Å / Num. obs: 26432 / % possible obs: 90 % / Observed criterion σ(I): 0 / Redundancy: 2.4 % / Biso Wilson estimate: 50.1 Å2 / Rsym value: 0.073 / Net I/σ(I): 21
Reflection shellResolution: 2.27→2.42 Å / Redundancy: 1.5 % / Mean I/σ(I) obs: 1.5 / Rsym value: 0.436 / % possible all: 52.6
Reflection
*PLUS
Num. measured all: 64590 / Rmerge(I) obs: 0.073
Reflection shell
*PLUS
% possible obs: 52.6 % / Rmerge(I) obs: 0.436

-
Processing

Software
NameVersionClassification
XENGENdata collection
XENGENdata reduction
AMoREphasing
PHASESphasing
XTALVIEWrefinement
X-PLOR3.1refinement
XENGENdata scaling
RefinementMethod to determine structure: MIR, MOLECULAR REPLACEMENT
Starting model: C ALPHA COORDINATES OF PDB ENTRY 1BOY

1boy


Resolution: 2.4→8 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.297 2038 9.8 %RANDOM
Rwork0.217 ---
obs0.217 20860 85.6 %-
Displacement parametersBiso mean: 51 Å2
Baniso -1Baniso -2Baniso -3
1--1.49 Å20 Å20 Å2
2---0.39 Å20 Å2
3---1.88 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.43 Å0.34 Å
Luzzati d res low-5 Å
Luzzati sigma a0.57 Å0.51 Å
Refinement stepCycle: LAST / Resolution: 2.4→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3089 0 0 14 3103
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.013
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_deg1.8
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d27.1
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.55
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it4.281.5
X-RAY DIFFRACTIONx_mcangle_it6.912
X-RAY DIFFRACTIONx_scbond_it6.832
X-RAY DIFFRACTIONx_scangle_it10.322.5
Refine LS restraints NCS
Ens-IDDom-IDNCS model detailsRefine-IDRms dev position (Å)Weight position
11RESTRAINTSX-RAY DIFFRACTION0.340.1
22X-RAY DIFFRACTION0.680.3
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.399 256 10.1 %
Rwork0.376 2287 -
obs--63.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg27.1
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.55

+
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