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Basic information

Entry
Database: PDB / ID: 3ela
TitleCrystal structure of active site inhibited coagulation factor VIIA mutant in complex with soluble tissue factor
Components
  • (Coagulation factor VIIA ...Coagulation factor VII) x 2
  • Tissue factor
KeywordsHYDROLASE/HYDROLASE INHIBITOR / Serine protease / BLOOD CLOTTING / HYDROLASE-HYDROLASE INHIBITOR complex
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 / response to vitamin K / response to carbon dioxide / response to thyroxine / positive regulation of leukocyte chemotaxis / NGF-stimulated transcription / response to cholesterol / response to growth hormone / cytokine receptor activity / positive regulation of positive chemotaxis / Extrinsic Pathway of Fibrin Clot Formation / 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 / 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 / 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 / Peptidase S1A, coagulation factor VII/IX/X/C/Z / Coagulation factor-like, Gla domain superfamily / Coagulation Factor Xa inhibitory site / Laminin ...Tissue factor / Tissue factor, conserved site / Tissue factor signature. / Interferon/interleukin receptor domain / Interferon-alpha/beta receptor, fibronectin type III / Tissue factor / Peptidase S1A, coagulation factor VII/IX/X/C/Z / Coagulation factor-like, Gla 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 / 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
D-Phe-Phe-Arg Chloromethylketone / Chem-0Z6 / alpha-L-fucopyranose / alpha-D-glucopyranose / Coagulation factor VII / Tissue factor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsBjelke, J.R. / Fodje, M. / Svensson, L.A.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: Mechanism of the Ca2+-induced enhancement of the intrinsic factor VIIa activity
Authors: Bjelke, J.R. / Olsen, O.H. / Fodje, M. / Svensson, L.A. / Bang, S. / Bolt, G. / Kragelund, B.B. / Persson, E.
History
DepositionSep 21, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 4, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary / Version format compliance
Revision 1.2Feb 27, 2013Group: Other
Revision 1.3Oct 25, 2017Group: Data collection / Refinement description / Category: diffrn_source / software / Item: _diffrn_source.pdbx_synchrotron_site / _software.name
Revision 1.4Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_conn_type / 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_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_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Nov 10, 2021Group: Database references / Structure summary / Category: chem_comp / database_2 / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.6Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: Coagulation factor VIIA light chain
H: Coagulation factor VIIA heavy chain
T: Tissue factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,6547
Polymers68,7653
Non-polymers8884
Water3,855214
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5400 Å2
ΔGint-19 kcal/mol
Surface area23590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.361, 68.558, 78.817
Angle α, β, γ (deg.)90.00, 90.22, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Coagulation factor VIIA ... , 2 types, 2 molecules LH

#1: Protein Coagulation factor VIIA light chain / Coagulation factor VII


Mass: 17046.975 Da / Num. of mol.: 1 / Fragment: UNP residues 61-212
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: F7 / Plasmid: PEE-ACEDELTA36NJ / Cell (production host): CHO-K1 / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P08709, coagulation factor VIIa
#2: Protein Coagulation factor VIIA heavy chain / Coagulation factor VII


Mass: 28086.164 Da / Num. of mol.: 1 / Fragment: UNP residues 213-466 / Mutation: V158D,E296V,M298Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: F7 / Plasmid: PEE-ACEDELTA36NJ / Cell (production host): CHO-K1 / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P08709, coagulation factor VIIa

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Protein , 1 types, 1 molecules T

#3: Protein Tissue factor / / TF / Coagulation factor III / Thromboplastin


Mass: 23632.195 Da / Num. of mol.: 1 / Fragment: UNP residues 33-241
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: F3 / Plasmid: pET_TF1-209 / Production host: Escherichia coli (E. coli) / References: UniProt: P13726

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Sugars , 2 types, 2 molecules

#4: 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
#5: 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 , 3 types, 216 molecules

#6: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#7: Chemical ChemComp-0Z6 / D-phenylalanyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexan-3-yl]-L-phenylalaninamide / FFRCK


Type: peptide-like, Peptide-like / Class: Inhibitor / Mass: 504.045 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H36ClN6O3 / References: D-Phe-Phe-Arg Chloromethylketone
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 214 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer detailsTHE UNBOUND FORM OF THE INHIBITOR IS D-PHE-PHE-ARG-CHLOROMETHYLKETONE. UPON REACTION WITH PROTEIN ...THE UNBOUND FORM OF THE INHIBITOR IS D-PHE-PHE-ARG-CHLOROMETHYLKETONE. UPON REACTION WITH PROTEIN IT FORMS TWO COVALENT BONDS: 1) A COVALENT BOND TO SER 344 H FORMING A HEMIKETAL AR7 AND 2) A COVALENT BOND TO NE2 OF HIS 193 H

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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: 3.06 Å3/Da / Density % sol: 59.77 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 100mM NaCitrate, 16%(w/v) PEG4000, 12%(v/v) 1-propanol, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 1.08 Å
DetectorDetector: CCD
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 2.2→29.19 Å / Num. all: 34658 / Num. obs: 34658 / % possible obs: 80.3 % / Redundancy: 1.8 % / Biso Wilson estimate: 23.5 Å2 / Rmerge(I) obs: 0.096
Reflection shellResolution: 2.2→2.3 Å / Redundancy: 1.3 % / Rmerge(I) obs: 0.229 / Mean I/σ(I) obs: 2.12 / Num. unique all: 1526 / % possible all: 26.1

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Processing

Software
NameVersionClassification
MAR345data collection
CCP4model building
MOLREPphasing
REFMAC5.2.0005refinement
XDSdata reduction
XDSdata scaling
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1DAN

1dan


Resolution: 2.2→29.19 Å / Cor.coef. Fo:Fc: 0.909 / Cor.coef. Fo:Fc free: 0.839 / SU B: 10.241 / SU ML: 0.237 / Cross valid method: THROUGHOUT / ESU R: 0.283 / ESU R Free: 0.242 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2943 1734 5 %RANDOM
Rwork0.23259 ---
obs0.23568 32936 100 %-
all-34719 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.911 Å2
Baniso -1Baniso -2Baniso -3
1--2.13 Å20 Å20.61 Å2
2---2.32 Å20 Å2
3---4.46 Å2
Refinement stepCycle: LAST / Resolution: 2.2→29.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4119 0 56 214 4389
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0224280
X-RAY DIFFRACTIONr_angle_refined_deg2.171.9525840
X-RAY DIFFRACTIONr_dihedral_angle_1_deg11.675537
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.32724.348184
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.40315643
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.6541521
X-RAY DIFFRACTIONr_chiral_restr0.1340.2663
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023252
X-RAY DIFFRACTIONr_nbd_refined0.2750.22118
X-RAY DIFFRACTIONr_nbtor_refined0.3190.22843
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2190.2325
X-RAY DIFFRACTIONr_metal_ion_refined0.160.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.5260.234
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3080.26
X-RAY DIFFRACTIONr_mcbond_it0.9581.52751
X-RAY DIFFRACTIONr_mcangle_it1.66724352
X-RAY DIFFRACTIONr_scbond_it2.12431747
X-RAY DIFFRACTIONr_scangle_it3.1714.51488
LS refinement shellResolution: 2.202→2.259 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.579 42 -
Rwork0.477 801 -
obs--100 %

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