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- PDB-6tkg: Tsetse thrombin inhibitor in complex with human alpha-thrombin - ... -

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Basic information

Entry
Database: PDB / ID: 6tkg
TitleTsetse thrombin inhibitor in complex with human alpha-thrombin - orthorhombic form at 12keV
Components
  • (Prothrombin) x 2
  • Tsetse thrombin inhibitor
KeywordsBLOOD CLOTTING / anticoagulant tyrosine sulfation posttranslational modification complex
Function / homology
Function and homology information


positive regulation of lipid kinase activity / positive regulation of phospholipase C-activating G protein-coupled receptor signaling pathway / cytolysis by host of symbiont cells / thrombospondin receptor activity / Defective factor XII causes hereditary angioedema / thrombin / regulation of blood coagulation / neutrophil-mediated killing of gram-negative bacterium / ligand-gated ion channel signaling pathway / Defective F8 cleavage by thrombin ...positive regulation of lipid kinase activity / positive regulation of phospholipase C-activating G protein-coupled receptor signaling pathway / cytolysis by host of symbiont cells / thrombospondin receptor activity / Defective factor XII causes hereditary angioedema / thrombin / regulation of blood coagulation / neutrophil-mediated killing of gram-negative bacterium / ligand-gated ion channel signaling pathway / Defective F8 cleavage by thrombin / Platelet Aggregation (Plug Formation) / negative regulation of astrocyte differentiation / negative regulation of platelet activation / positive regulation of collagen biosynthetic process / negative regulation of cytokine production involved in inflammatory response / positive regulation of blood coagulation / negative regulation of fibrinolysis / Gamma-carboxylation of protein precursors / Transport of gamma-carboxylated protein precursors from the endoplasmic reticulum to the Golgi apparatus / Common Pathway of Fibrin Clot Formation / Removal of aminoterminal propeptides from gamma-carboxylated proteins / fibrinolysis / regulation of cytosolic calcium ion concentration / Intrinsic Pathway of Fibrin Clot Formation / Peptide ligand-binding receptors / positive regulation of release of sequestered calcium ion into cytosol / acute-phase response / Regulation of Complement cascade / negative regulation of proteolysis / Cell surface interactions at the vascular wall / lipopolysaccharide binding / positive regulation of receptor signaling pathway via JAK-STAT / growth factor activity / serine-type endopeptidase inhibitor activity / positive regulation of insulin secretion / platelet activation / response to wounding / positive regulation of protein localization to nucleus / Golgi lumen / antimicrobial humoral immune response mediated by antimicrobial peptide / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / positive regulation of reactive oxygen species metabolic process / blood coagulation / Thrombin signalling through proteinase activated receptors (PARs) / heparin binding / regulation of cell shape / positive regulation of cell growth / G alpha (q) signalling events / collagen-containing extracellular matrix / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cell surface receptor signaling pathway / blood microparticle / positive regulation of protein phosphorylation / G protein-coupled receptor signaling pathway / endoplasmic reticulum lumen / serine-type endopeptidase activity / signaling receptor binding / calcium ion binding / positive regulation of cell population proliferation / proteolysis / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
Prothrombin/thrombin / Thrombin light chain / Thrombin light chain domain superfamily / Thrombin light chain / Kringle domain / Kringle / Kringle, conserved site / Kringle superfamily / Kringle domain signature. / Kringle domain profile. ...Prothrombin/thrombin / Thrombin light chain / Thrombin light chain domain superfamily / Thrombin light chain / Kringle domain / Kringle / Kringle, conserved site / Kringle superfamily / Kringle domain signature. / Kringle domain profile. / Kringle 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. / Kringle-like fold / 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 / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan
Similarity search - Domain/homology
Tsetse thrombin inhibitor / Prothrombin
Similarity search - Component
Biological speciesHomo sapiens (human)
Glossina morsitans morsitans (fry)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsCalisto, B.M. / Ripoll-Rozada, J. / de Sanctis, D. / Pereira, P.J.B.
Funding support Australia, Portugal, 2items
OrganizationGrant numberCountry
National Health and Medical Research Council (Australia)APP1120941 Australia
Fundacao para a Ciencia e a Tecnologia57/2016/CP1355/CT0011 Portugal
CitationJournal: Cell Chem Biol / Year: 2021
Title: Sulfotyrosine-Mediated Recognition of Human Thrombin by a Tsetse Fly Anticoagulant Mimics Physiological Substrates.
Authors: Calisto, B.M. / Ripoll-Rozada, J. / Dowman, L.J. / Franck, C. / Agten, S.M. / Parker, B.L. / Veloso, R.C. / Vale, N. / Gomes, P. / de Sanctis, D. / Payne, R.J. / Pereira, P.J.B.
History
DepositionNov 28, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 4, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 3, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.year
Revision 1.2Jan 24, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_residues
Item: _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: Prothrombin
H: Prothrombin
I: Tsetse thrombin inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,1766
Polymers39,8403
Non-polymers3363
Water5,585310
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6600 Å2
ΔGint-28 kcal/mol
Surface area13350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.438, 81.124, 85.544
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Protein , 2 types, 2 molecules HI

#2: Protein Prothrombin / Coagulation factor II


Mass: 29780.219 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P00734, thrombin
#3: Protein Tsetse thrombin inhibitor


Mass: 5962.750 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: Residues 9 and 12 of the mature sequence are O-sulfated.
Source: (synth.) Glossina morsitans morsitans (fry) / References: UniProt: O97373

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Protein/peptide / Sugars , 2 types, 2 molecules L

#1: Protein/peptide Prothrombin / Coagulation factor II


Mass: 4096.534 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P00734, thrombin
#4: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 312 molecules

#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 310 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.23 Å3/Da / Density % sol: 44.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M HEPES pH 7.5, 0.2 M ammonium acetate, 25 % (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 1.033 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 20, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 1.35→58.9 Å / Num. obs: 70747 / % possible obs: 98.5 % / Redundancy: 5.4 % / Biso Wilson estimate: 17.3 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.073 / Net I/σ(I): 9.7
Reflection shellResolution: 1.35→1.37 Å / Redundancy: 5 % / Rmerge(I) obs: 2.34 / Mean I/σ(I) obs: 0.5 / Num. unique obs: 3266 / CC1/2: 0.421 / % possible all: 91.3

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3U69

3u69


Resolution: 1.35→42.77 Å / SU ML: 0.2059 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 25.2386
RfactorNum. reflection% reflection
Rfree0.195 3396 4.81 %
Rwork0.1641 --
obs0.1657 70550 98.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 27.88 Å2
Refinement stepCycle: LAST / Resolution: 1.35→42.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2519 0 21 310 2850
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00742661
X-RAY DIFFRACTIONf_angle_d0.94593607
X-RAY DIFFRACTIONf_chiral_restr0.0885374
X-RAY DIFFRACTIONf_plane_restr0.006471
X-RAY DIFFRACTIONf_dihedral_angle_d28.86651031
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.35-1.370.43081310.39622525X-RAY DIFFRACTION89.04
1.37-1.390.36691310.35462742X-RAY DIFFRACTION97.13
1.39-1.410.3431280.32522754X-RAY DIFFRACTION97.17
1.41-1.430.36741370.30662731X-RAY DIFFRACTION97.25
1.43-1.460.30111450.30552760X-RAY DIFFRACTION97.58
1.46-1.480.36761470.27942718X-RAY DIFFRACTION97.58
1.48-1.510.33231350.26062759X-RAY DIFFRACTION97.94
1.51-1.540.25221310.23852784X-RAY DIFFRACTION97.75
1.54-1.580.29861250.20952749X-RAY DIFFRACTION97.69
1.58-1.610.27281460.19942783X-RAY DIFFRACTION98.16
1.61-1.650.26291210.18452792X-RAY DIFFRACTION97.88
1.65-1.70.20161090.17672806X-RAY DIFFRACTION98.61
1.7-1.750.2631260.16492803X-RAY DIFFRACTION98.42
1.75-1.810.1941290.15912816X-RAY DIFFRACTION98.26
1.81-1.870.20731700.15582791X-RAY DIFFRACTION98.96
1.87-1.950.18821380.14682828X-RAY DIFFRACTION98.9
1.95-2.030.19031480.14052814X-RAY DIFFRACTION99.03
2.03-2.140.16721660.13752793X-RAY DIFFRACTION99.36
2.14-2.280.19771230.13482869X-RAY DIFFRACTION99.5
2.28-2.450.16891640.14482852X-RAY DIFFRACTION99.54
2.45-2.70.20111470.1572856X-RAY DIFFRACTION99.44
2.7-3.090.19161570.15482897X-RAY DIFFRACTION99.84
3.09-3.890.15421780.13912902X-RAY DIFFRACTION99.61
3.89-42.770.16281640.15083030X-RAY DIFFRACTION99.13

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