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- PDB-1fak: HUMAN TISSUE FACTOR COMPLEXED WITH COAGULATION FACTOR VIIA INHIBI... -

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Basic information

Entry
Database: PDB / ID: 1fak
TitleHUMAN TISSUE FACTOR COMPLEXED WITH COAGULATION FACTOR VIIA INHIBITED WITH A BPTI-MUTANT
Components
  • (PROTEIN (BLOOD COAGULATION FACTOR ...) x 2
  • PROTEIN (5L15)
  • PROTEIN (SOLUBLE TISSUE FACTOR)
KeywordsBLOOD CLOTTING / COMPLEX(SERINE PROTEASE-COFACTOR-LIGAND) / BLOOD COAGULATION / SERINE PROTEASE / COMPLEX / CO-FACTOR / RECEPTOR ENZYME / INHIBITOR / GLA / EGF / COMPLEX (SERINE PROTEASE-COFACTOR-LIGAND)
Function / homology
Function and homology information


activation of plasma proteins involved in acute inflammatory response / activation of blood coagulation via clotting cascade / coagulation factor VIIa / response to Thyroid stimulating hormone / response to 2,3,7,8-tetrachlorodibenzodioxine / response to astaxanthin / response to thyrotropin-releasing hormone / response to genistein / serine-type peptidase complex / positive regulation of platelet-derived growth factor receptor signaling pathway ...activation of plasma proteins involved in acute inflammatory response / activation of blood coagulation via clotting cascade / coagulation factor VIIa / response to Thyroid stimulating hormone / response to 2,3,7,8-tetrachlorodibenzodioxine / response to astaxanthin / response to thyrotropin-releasing hormone / response to genistein / serine-type peptidase complex / positive regulation of platelet-derived growth factor receptor signaling pathway / trypsinogen activation / response to vitamin K / negative regulation of serine-type endopeptidase activity / response to carbon dioxide / sulfate binding / response to thyroxine / positive regulation of leukocyte chemotaxis / potassium channel inhibitor activity / negative regulation of platelet aggregation / zymogen binding / NGF-stimulated transcription / response to cholesterol / response to growth hormone / cytokine receptor activity / positive regulation of positive chemotaxis / Extrinsic Pathway of Fibrin Clot Formation / molecular function inhibitor activity / negative regulation of thrombin-activated receptor signaling pathway / positive regulation of TOR signaling / positive regulation of blood coagulation / animal organ regeneration / Gamma-carboxylation of protein precursors / Transport of gamma-carboxylated protein precursors from the endoplasmic reticulum to the Golgi apparatus / Removal of aminoterminal propeptides from gamma-carboxylated proteins / serine protease inhibitor complex / positive regulation of endothelial cell proliferation / serine-type peptidase activity / BMAL1:CLOCK,NPAS2 activates circadian gene expression / positive regulation of interleukin-8 production / phospholipid binding / serine-type endopeptidase inhibitor activity / protein processing / Golgi lumen / cytokine-mediated signaling pathway / circadian rhythm / response to estrogen / activation of cysteine-type endopeptidase activity involved in apoptotic process / positive regulation of angiogenesis / blood coagulation / response to estradiol / collagen-containing extracellular matrix / protease binding / vesicle / response to hypoxia / positive regulation of cell migration / endoplasmic reticulum lumen / external side of plasma membrane / signaling receptor binding / serine-type endopeptidase activity / calcium ion binding / positive regulation of gene expression / cell surface / extracellular space / extracellular region / 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 / Pancreatic trypsin inhibitor Kunitz domain / Factor Xa Inhibitor / Peptidase S1A, coagulation factor VII/IX/X/C/Z / Coagulation factor-like, Gla domain superfamily ...Tissue factor / Tissue factor, conserved site / Tissue factor signature. / Interferon/interleukin receptor domain / Interferon-alpha/beta receptor, fibronectin type III / Tissue factor / Pancreatic trypsin inhibitor Kunitz domain / Factor Xa Inhibitor / Peptidase S1A, coagulation factor VII/IX/X/C/Z / Coagulation factor-like, Gla domain superfamily / Proteinase inhibitor I2, Kunitz, conserved site / Pancreatic trypsin inhibitor (Kunitz) family signature. / BPTI/Kunitz family of serine protease inhibitors. / Pancreatic trypsin inhibitor Kunitz domain / Kunitz/Bovine pancreatic trypsin inhibitor domain / Pancreatic trypsin inhibitor (Kunitz) family profile. / Pancreatic trypsin inhibitor Kunitz domain superfamily / Coagulation Factor Xa inhibitory site / Laminin / Laminin / EGF-type aspartate/asparagine hydroxylation site / EGF-like domain / EGF-like calcium-binding, conserved site / Calcium-binding EGF-like domain signature. / Aspartic acid and asparagine hydroxylation site. / EGF-like calcium-binding domain / Calcium-binding EGF-like domain / Vitamin K-dependent carboxylation/gamma-carboxyglutamic (GLA) domain / Gamma-carboxyglutamic acid-rich (GLA) domain / Gamma-carboxyglutamic acid-rich (GLA) domain superfamily / Vitamin K-dependent carboxylation domain. / Gla domain profile. / Domain containing Gla (gamma-carboxyglutamate) residues. / Epidermal growth factor-like domain. / EGF-like domain profile. / EGF-like domain signature 2. / EGF-like domain signature 1. / EGF-like domain / Fibronectin type III / Fibronectin type III superfamily / Ribbon / Few Secondary Structures / Irregular / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin domain profile. / Serine proteases, trypsin family, serine active site. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases / Thrombin, subunit H / Immunoglobulins / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Immunoglobulin-like fold / Immunoglobulin-like / Beta Barrel / Sandwich / Mainly Beta
Similarity search - Domain/homology
alpha-L-fucopyranose / alpha-D-glucopyranose / Pancreatic trypsin inhibitor / Coagulation factor VII / Tissue factor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsZhang, E. / St Charles, R. / Tulinsky, A.
CitationJournal: J.Mol.Biol. / Year: 1999
Title: Structure of extracellular tissue factor complexed with factor VIIa inhibited with a BPTI mutant.
Authors: Zhang, E. / St Charles, R. / Tulinsky, A.
History
DepositionDec 28, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Dec 3, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / database_PDB_caveat ...chem_comp / database_PDB_caveat / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4May 31, 2023Group: Database references / Structure summary / Category: chem_comp / database_2
Item: _chem_comp.pdbx_synonyms / _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
L: PROTEIN (BLOOD COAGULATION FACTOR VIIA)
H: PROTEIN (BLOOD COAGULATION FACTOR VIIA)
T: PROTEIN (SOLUBLE TISSUE FACTOR)
I: PROTEIN (5L15)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,7318
Polymers75,3074
Non-polymers4244
Water6,125340
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7610 Å2
ΔGint-33 kcal/mol
Surface area26790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.490, 190.000, 175.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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PROTEIN (BLOOD COAGULATION FACTOR ... , 2 types, 2 molecules LH

#1: Protein PROTEIN (BLOOD COAGULATION FACTOR VIIA)


Mass: 17487.076 Da / Num. of mol.: 1 / Fragment: LIGHT CHAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): KIDNEY CELLS (BHK) / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P08709, coagulation factor VIIa
#2: Protein PROTEIN (BLOOD COAGULATION FACTOR VIIA)


Mass: 28103.256 Da / Num. of mol.: 1 / Fragment: HEAVY CHAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): KIDNEY CELLS (BHK) / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P08709, coagulation factor VIIa

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Protein , 2 types, 2 molecules TI

#3: Protein PROTEIN (SOLUBLE TISSUE FACTOR)


Mass: 23417.053 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P13726
#4: Protein PROTEIN (5L15)


Mass: 6299.163 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Chemically synthesized / References: UniProt: P00974

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Sugars , 2 types, 2 molecules

#5: Sugar ChemComp-GLC / alpha-D-glucopyranose / alpha-D-glucose / D-glucose / glucose / Glucose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-glucopyranoseCOMMON NAMEGMML 1.0
a-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#6: Sugar ChemComp-FUC / alpha-L-fucopyranose / alpha-L-fucose / 6-deoxy-alpha-L-galactopyranose / L-fucose / fucose / Fucose


Type: L-saccharide, alpha linking / Mass: 164.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O5
IdentifierTypeProgram
LFucpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-L-fucopyranoseCOMMON NAMEGMML 1.0
a-L-FucpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
FucSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 2 types, 342 molecules

#7: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 340 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 3.68 Å3/Da / Density % sol: 64 %
Crystal growpH: 5.6 / Details: pH 5.6
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
10.1 Msodium citrate1reservoirpH5.6
216.0-16.5 %(w/v)PEG40001reservoir
312 %(v/v)1-propanol1reservoir
43.4 mg/mlprotein1drop
515 mMTris-HCl1drop
625 mMsodium citrate1drop
737.5 mM1dropNaCl
81.5 mM1dropCaCl2
94 %(w/v)PEG40001drop
103 %(v/v)1-propanol1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 0.89
DetectorType: SIEMENS / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.89 Å / Relative weight: 1
ReflectionResolution: 2.1→20 Å / Num. obs: 61209 / % possible obs: 87 % / Observed criterion σ(I): 1 / Redundancy: 2.35 % / Rmerge(I) obs: 0.094
Reflection
*PLUS
Num. obs: 70671 / Num. measured all: 166318
Reflection shell
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 2.2 Å / % possible obs: 78 % / Num. unique obs: 61209

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Processing

Software
NameClassification
SAINTdata scaling
SAINTdata reduction
AMoREphasing
PROLSQrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→9 Å / σ(F): 0 /
RfactorNum. reflection% reflection
obs0.237 49719 80 %
Refinement stepCycle: LAST / Resolution: 2.1→9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4716 0 23 340 5079
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0220.02
X-RAY DIFFRACTIONp_angle_d0.0410.03
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0540.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.451.5
X-RAY DIFFRACTIONp_mcangle_it2.142
X-RAY DIFFRACTIONp_scbond_it3.833
X-RAY DIFFRACTIONp_scangle_it4.925
X-RAY DIFFRACTIONp_plane_restr0.0130.015
X-RAY DIFFRACTIONp_chiral_restr0.2190.15
X-RAY DIFFRACTIONp_singtor_nbd0.1950.6
X-RAY DIFFRACTIONp_multtor_nbd0.2380.6
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.2470.6
X-RAY DIFFRACTIONp_planar_tor3.11.5
X-RAY DIFFRACTIONp_staggered_tor2120
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor20.925
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROLSQ / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.1 Å / σ(F): 0
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0220.02
X-RAY DIFFRACTIONp_angle_d0.0410.03
X-RAY DIFFRACTIONp_planar_d0.0540.05
X-RAY DIFFRACTIONp_plane_restr0.0130.015
X-RAY DIFFRACTIONp_chiral_restr0.2190.15
X-RAY DIFFRACTIONp_mcbond_it1.451.5
X-RAY DIFFRACTIONp_scbond_it3.833
X-RAY DIFFRACTIONp_mcangle_it2.142
X-RAY DIFFRACTIONp_scangle_it4.925

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