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- PDB-4zma: Crystal Structure of a FVIIa-Trypsin Chimera (ST) in Complex with... -

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Basic information

Entry
Database: PDB / ID: 4zma
TitleCrystal Structure of a FVIIa-Trypsin Chimera (ST) in Complex with Soluble Tissue Factor
Components
  • (Coagulation factor ...) x 2
  • Tissue factor
KeywordsHYDROLASE / fusion protein / trypsin-fold / protein-protein 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 astaxanthin / response to thyrotropin-releasing hormone / response to 2,3,7,8-tetrachlorodibenzodioxine / response to genistein / serine-type peptidase complex / response to carbon dioxide ...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 astaxanthin / response to thyrotropin-releasing hormone / response to 2,3,7,8-tetrachlorodibenzodioxine / response to genistein / serine-type peptidase complex / response to carbon dioxide / response to vitamin K / response to thyroxine / positive regulation of platelet-derived growth factor receptor signaling pathway / positive regulation of leukocyte chemotaxis / NGF-stimulated transcription / response to cholesterol / cytokine receptor activity / response to growth hormone / positive regulation of positive chemotaxis / Extrinsic Pathway of Fibrin Clot Formation / positive regulation of endothelial cell apoptotic process / positive regulation of blood coagulation / positive regulation of TOR signaling / animal organ regeneration / Transport of gamma-carboxylated protein precursors from the endoplasmic reticulum to the Golgi apparatus / Gamma-carboxylation of protein precursors / Removal of aminoterminal propeptides from gamma-carboxylated proteins / positive regulation of endothelial cell proliferation / serine-type peptidase activity / BMAL1:CLOCK,NPAS2 activates circadian expression / positive regulation of interleukin-8 production / cytokine-mediated signaling pathway / protein processing / phospholipid binding / Golgi lumen / response to estrogen / circadian rhythm / positive regulation of angiogenesis / blood coagulation / response to estradiol / 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 ...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 / EGF-like domain / EGF-type aspartate/asparagine hydroxylation site / 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 1. / EGF-like domain signature 2. / EGF-like domain / Fibronectin type III / Fibronectin type III superfamily / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Serine proteases, trypsin family, histidine active site. / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases / Thrombin, subunit H / Peptidase S1, PA clan, chymotrypsin-like fold / Immunoglobulin-like fold / Peptidase S1, PA clan / Immunoglobulins / Beta Barrel / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
D-Phe-Phe-Arg Chloromethylketone / Chem-0Z6 / beta-D-glucopyranose / CACODYLATE ION / alpha-L-fucopyranose / Coagulation factor VII / Tissue factor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
Model detailsA human-FVIIa Variant with the 170-loop swapped with that from human-Trypsin, and an additional ...A human-FVIIa Variant with the 170-loop swapped with that from human-Trypsin, and an additional replacement of Tyr170b with Phe
AuthorsSorensen, A.B. / Svensson, L.A. / Gandhi, P.S.
CitationJournal: J.Biol.Chem. / Year: 2016
Title: Molecular Basis of Enhanced Activity in Factor VIIa-Trypsin Variants Conveys Insights into Tissue Factor-mediated Allosteric Regulation of Factor VIIa Activity.
Authors: Sorensen, A.B. / Madsen, J.J. / Svensson, L.A. / Pedersen, A.A. / stergaard, H. / Overgaard, M.T. / Olsen, O.H. / Gandhi, P.S.
History
DepositionMay 2, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Dec 30, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 13, 2016Group: Database references
Revision 1.2Mar 9, 2016Group: Database references
Revision 1.3Dec 21, 2016Group: Non-polymer description
Revision 1.4Jan 17, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / 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: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _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.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_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: Coagulation factor VII
H: Coagulation factor VII
T: Tissue factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,20516
Polymers69,7623
Non-polymers1,44313
Water3,873215
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6920 Å2
ΔGint-78 kcal/mol
Surface area26750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.209, 80.898, 125.759
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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

#1: Protein Coagulation factor VII / Proconvertin / Serum prothrombin conversion accelerator / SPCA


Mass: 17487.076 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Tissue: Blood / Gene: F7 / Organ: Kidney / Plasmid: pQMCF-5
Details (production host): Cells were licensed from Icosagen (Estonia)
Cell line (production host): CHOEBNALT85 / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P08709, coagulation factor VIIa
#2: Protein Coagulation factor VII / Proconvertin / Serum prothrombin conversion accelerator / SPCA


Mass: 27448.516 Da / Num. of mol.: 1 / Fragment: UNP residues 213-466 / Mutation: 169-175 LQQSRKVGDSPN -> EASSPGK
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Tissue: Blood / Gene: F7 / Organ: Kidney / Plasmid: pQMCF-5
Details (production host): Cells were licensed from Icosagen (Estonia)
Cell line (production host): CHOEBNALT85 / 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: 24826.512 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Tissue: Blood / Gene: F3 / Plasmid: pET3a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Origami 2 / References: UniProt: P13726

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Sugars , 2 types, 2 molecules

#5: Sugar ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranoseCOMMON NAMEGMML 1.0
b-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


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 , 4 types, 226 molecules

#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / 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 / Mutation: 169-175] LQQSRKVGDSPN -> EASSPGK
Source method: isolated from a genetically manipulated source
Formula: C25H36ClN6O3
References: D-Phe-Phe-Arg Chloromethylketone, coagulation factor VIIa
#8: Chemical ChemComp-CAC / CACODYLATE ION / Proconvertin / Serum prothrombin conversion accelerator / SPCA / dimethylarsinate


Mass: 136.989 Da / Num. of mol.: 2 / Mutation: 169-175] LQQSRKVGDSPN -> EASSPGK
Source method: isolated from a genetically manipulated source
Formula: C2H6AsO2 / Source: (gene. exp.) Homo sapiens (human) / Tissue: Blood / Gene: F7 / Organ: Kidney / Plasmid: pQMCF-5
Details (production host): Cells were licensed from Icosagen (Estonia)
Cell line (production host): CHOEBNALT85 / Production host: Cricetulus griseus (Chinese hamster) / References: coagulation factor VIIa
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 215 / 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: 2.51 Å3/Da / Density % sol: 51.08 % / Description: Elongated hexgonal prisms
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.1 / Details: 0.1M Cacodylate,11% PEG 8000 , with seeding

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 5, 2013
Details: Rh-coated Si mirrors: M1 collimating mirror, M2 toroidal focusing mirror
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→29.77 Å / Num. all: 29510 / Num. obs: 29510 / % possible obs: 96 % / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Rmerge(I) obs: 0.1571 / Net I/σ(I): 8.65
Reflection shellResolution: 2.3→2.382 Å / Redundancy: 3.2 % / Rmerge(I) obs: 1.92 / Mean I/σ(I) obs: 0.78 / % possible all: 87

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Processing

Software
NameVersionClassification
PHENIXrefinement
XDSMarch 30, 2013data reduction
XSCALEJuly 4, 2012 BUILT=20130706data scaling
PHASER2.5.7phasing
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: In-House FVIIa-WT:sTF-FFR similar to 1DAN

1dan


Resolution: 2.3→29.768 Å / SU ML: 0.45 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 33.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2947 1500 5.08 %Random selection
Rwork0.2401 28010 --
obs0.2429 29510 96.11 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 90.01 Å2 / Biso mean: 41.399 Å2 / Biso min: 10.33 Å2
Refinement stepCycle: final / Resolution: 2.3→29.768 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4565 0 58 215 4838
Biso mean--57.5 33.79 -
Num. residues----587
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0174802
X-RAY DIFFRACTIONf_angle_d0.5886433
X-RAY DIFFRACTIONf_chiral_restr0.026722
X-RAY DIFFRACTIONf_plane_restr0.002830
X-RAY DIFFRACTIONf_dihedral_angle_d10.6231669
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3-2.37420.4281230.3692283240687
2.3742-2.4590.35061340.35082484261896
2.459-2.55740.42851320.32682539267197
2.5574-2.67380.39661420.3092518266097
2.6738-2.81460.35031480.29092554270298
2.8146-2.99080.33521350.2772564269997
2.9908-3.22150.3131400.2562564270498
3.2215-3.54520.30821330.22272585271898
3.5452-4.05710.26021360.20422617275398
4.0571-5.10730.20331560.17592628278498
5.1073-29.77020.26041210.20852674279594

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