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- PDB-6r2w: Crystal structure of the super-active FVIIa variant VYT in comple... -

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Basic information

Entry
Database: PDB / ID: 6r2w
TitleCrystal structure of the super-active FVIIa variant VYT in complex with tissue factor
Components
  • (Coagulation factor ...) x 2
  • Tissue factor
KeywordsHYDROLASE / TRYPSIN-FOLD / PROTEIN-PROTEIN COMPLEX / COAGULATION FACTOR
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
Chem-0Z7 / alpha-L-fucopyranose / TETRAMETHYLAMMONIUM ION / Coagulation factor VII / Tissue factor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å
AuthorsSorensen, A.B. / Svensson, L.A. / Gandhi, P.S.
CitationJournal: J.Biol.Chem. / Year: 2020
Title: Beating tissue factor at its own game: Design and properties of a soluble tissue factor-independent coagulation factor VIIa.
Authors: Sorensen, A.B. / Tuneew, I. / Svensson, L.A. / Persson, E. / Ostergaard, H. / Overgaard, M.T. / Olsen, O.H. / Gandhi, P.S.
History
DepositionMar 19, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 11, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Jan 22, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Refinement description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_validate_close_contact / refine / struct_asym / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.id / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_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 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_2 / _refine.pdbx_diffrn_id / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr2_label_alt_id / _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 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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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)70,02025
Polymers67,7633
Non-polymers2,25722
Water12,863714
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry, surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10190 Å2
ΔGint-57 kcal/mol
Surface area27250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.310, 80.040, 123.380
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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: 16488.953 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 / 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: 27510.584 Da / Num. of mol.: 1
Mutation: L350V,371-375del,K376E,V377A,G378S,D379Y,S380P,P381G,N382K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Tissue: BLOOD / Gene: F7 / Organ: KIDNEY / Plasmid: PQMCF-5 / 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: 23763.393 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

#4: Polysaccharide alpha-D-xylopyranose-(1-3)-alpha-D-xylopyranose-(1-3)-beta-D-glucopyranose


Type: oligosaccharide / Mass: 444.386 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DXylpa1-3DXylpa1-3DGlcpb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5][a212h-1a_1-5]/1-2-2/a3-b1_b3-c1WURCSPDB2Glycan 1.1.0
[]{[(3+1)][b-D-Glcp]{[(3+1)][a-D-Xylp]{[(3+1)][a-D-Xylp]{}}}}LINUCSPDB-CARE
#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, 734 molecules

#5: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Ca
#7: Chemical
ChemComp-TMA / TETRAMETHYLAMMONIUM ION


Mass: 74.145 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Formula: C4H12N
#8: Chemical ChemComp-0Z7 / N-acetyl-D-phenylalanyl-N-[(2S,3S)-6-carbamimidamido-1-chloro-2-hydroxyhexan-3-yl]-L-phenylalaninamide


Mass: 546.081 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H38ClN6O4
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 714 / 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: 2.55 Å3/Da / Density % sol: 51.72 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.1 M sodium citrate, pH 5.6, 15.6 % (w/v) PEG 3350, 12 % (v/v) 1-Propanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 6, 2014
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.25→36.58 Å / Num. obs: 190625 / % possible obs: 97.8 % / Redundancy: 7.711 % / Biso Wilson estimate: 14.09 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.098 / Rrim(I) all: 0.105 / Χ2: 0.985 / Net I/σ(I): 12.26 / Num. measured all: 1469961 / Scaling rejects: 4252
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.25-1.33.7213.5420.447570521380203460.1364.13595.2
1.3-1.353.7292.5160.626583418378176530.2152.93696.1
1.35-1.43.7341.8680.835716015868153100.3012.1896.5
1.4-1.456.0061.531.38010413751133370.451.67597
1.45-1.58.7231.311.9210211711999117060.6381.39197.6
1.5-1.559.5780.9922.79842810506102770.7781.04797.8
1.55-1.69.6640.7673.5487734926290780.8660.8198
1.6-1.79.6810.5454.914658615398151420.920.57498.3
1.7-1.89.690.3547.411597612131119690.9640.37398.7
1.8-29.6730.20312.1916936817692175090.9880.21499
2-2.59.6150.09623.6122359623374232540.9970.10199.5
2.5-39.540.05337.359892410389103690.9990.05699.8
3-49.4060.03454.5778634836483600.9990.036100
4-69.2580.02766.6404294374436710.02999.8
6-1015.6260.03972.82235331509150610.0499.8
10-36.5813.1970.02780.35583345544210.02997.1

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
XDSMarch 30, 2013data reduction
XSCALEJuly 4, 2012 BUILT=20130706data scaling
PHASER2.5.7phasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1DAN

1dan


Resolution: 1.25→36.58 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.32 / Phase error: 25.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1938 9562 5.02 %
Rwork0.1702 180980 -
obs0.1714 190542 97.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 119.9 Å2 / Biso mean: 27.0879 Å2 / Biso min: 4.36 Å2
Refinement stepCycle: final / Resolution: 1.25→36.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4786 0 253 714 5753
Biso mean--52.49 33.92 -
Num. residues----603
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.25-1.26420.44422980.4195671596993
1.2642-1.27910.41462690.40465886615595
1.2791-1.29470.4173300.38495807613795
1.2947-1.3110.38523030.36875850615396
1.311-1.32830.34023240.3575853617796
1.3283-1.34650.37363140.34885862617696
1.3465-1.36570.35313210.33575881620296
1.3657-1.38610.33843350.34025879621497
1.3861-1.40780.35663160.31165948626497
1.4078-1.43090.29873290.29185913624297
1.4309-1.45550.31052970.27396001629897
1.4555-1.4820.29513130.24965940625398
1.482-1.51050.26313110.2266025633698
1.5105-1.54130.23593040.20495988629298
1.5413-1.57490.23332940.18866038633298
1.5749-1.61150.21642940.1736015630998
1.6115-1.65180.19633110.16676097640898
1.6518-1.69640.2023170.16476027634498
1.6964-1.74640.19152970.15536087638499
1.7464-1.80270.19173030.15586096639999
1.8027-1.86720.18313610.14636057641899
1.8672-1.94190.18572970.1446140643799
1.9419-2.03030.16563280.13566139646799
2.0303-2.13730.16333160.13286139645599
2.1373-2.27120.16013740.130561436517100
2.2712-2.44650.16123560.130861706526100
2.4465-2.69270.1653410.136162086549100
2.6927-3.08210.17673280.140862826610100
3.0821-3.88250.1523370.138963006637100
3.8825-36.59590.15313440.149265386882100

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