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

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Basic information

Entry
Database: PDB / ID: 6tki
TitleTsetse thrombin inhibitor in complex with human alpha-thrombin - tetragonal form at 12.7keV
Components
  • Thrombin heavy chain
  • Thrombin light chain
  • Tsetse thrombin inhibitor
KeywordsBLOOD CLOTTING / anticoagulant tyrosine sulfation posttranslational modification complex
Function / homology
Function and homology information


cytolysis by host of symbiont cells / positive regulation of phospholipase C-activating G protein-coupled receptor signaling pathway / thrombospondin receptor activity / Defective factor XII causes hereditary angioedema / thrombin-activated receptor signaling pathway / thrombin / neutrophil-mediated killing of gram-negative bacterium / regulation of blood coagulation / Defective F8 cleavage by thrombin / ligand-gated ion channel signaling pathway ...cytolysis by host of symbiont cells / positive regulation of phospholipase C-activating G protein-coupled receptor signaling pathway / thrombospondin receptor activity / Defective factor XII causes hereditary angioedema / thrombin-activated receptor signaling pathway / thrombin / neutrophil-mediated killing of gram-negative bacterium / regulation of blood coagulation / Defective F8 cleavage by thrombin / ligand-gated ion channel signaling pathway / Platelet Aggregation (Plug Formation) / negative regulation of astrocyte differentiation / positive regulation of collagen biosynthetic process / negative regulation of platelet activation / negative regulation of blood coagulation / positive regulation of blood coagulation / negative regulation of fibrinolysis / regulation of cytosolic calcium ion concentration / Transport of gamma-carboxylated protein precursors from the endoplasmic reticulum to the Golgi apparatus / Gamma-carboxylation of protein precursors / Common Pathway of Fibrin Clot Formation / Removal of aminoterminal propeptides from gamma-carboxylated proteins / fibrinolysis / negative regulation of proteolysis / Intrinsic Pathway of Fibrin Clot Formation / negative regulation of cytokine production involved in inflammatory response / positive regulation of release of sequestered calcium ion into cytosol / Peptide ligand-binding receptors / Regulation of Complement cascade / acute-phase response / positive regulation of receptor signaling pathway via JAK-STAT / Cell surface interactions at the vascular wall / lipopolysaccharide binding / growth factor activity / serine-type endopeptidase inhibitor activity / positive regulation of insulin secretion / platelet activation / positive regulation of protein localization to nucleus / response to wounding / 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 / heparin binding / regulation of cell shape / Thrombin signalling through proteinase activated receptors (PARs) / positive regulation of protein phosphorylation / positive regulation of cell growth / : / G alpha (q) signalling events / blood microparticle / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cell surface receptor signaling pathway / receptor ligand activity / endoplasmic reticulum lumen / signaling receptor binding / serine-type endopeptidase activity / positive regulation of cell population proliferation / calcium ion binding / 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. ...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 / 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 / Peptidase S1, PA clan / Beta Barrel / Mainly Beta
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: 1.8 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: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: Thrombin light chain
H: Thrombin heavy chain
I: Tsetse thrombin inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,0845
Polymers39,8403
Non-polymers2442
Water3,045169
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5170 Å2
ΔGint-27 kcal/mol
Surface area12620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.696, 112.696, 60.207
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Components on special symmetry positions
IDModelComponents
11L-403-

HOH

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Components

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Protein , 2 types, 2 molecules HI

#2: Protein Thrombin heavy chain / 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 / Source: (synth.) Glossina morsitans morsitans (fry) / References: UniProt: O97373

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

#1: Protein/peptide Thrombin light chain / 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 , 2 types, 170 molecules

#5: Chemical ChemComp-NA / SODIUM ION


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


Mass: 18.015 Da / Num. of mol.: 169 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 2.92 Å3/Da / Density % sol: 57.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.05 M sodium cacodylate pH 6.5, 0.01 M magnesium sulfate, 2 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.976 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 15, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.8→79.7 Å / Num. obs: 36431 / % possible obs: 99.8 % / Redundancy: 6.5 % / Biso Wilson estimate: 31.16 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.066 / Net I/σ(I): 15.8
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 6.6 % / Rmerge(I) obs: 1.541 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 5163 / CC1/2: 0.604 / % possible all: 98.9

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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: 1.8→48.04 Å / SU ML: 0.2174 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 25.2622
RfactorNum. reflection% reflection
Rfree0.2143 1783 4.9 %
Rwork0.1812 --
obs0.1827 36353 99.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 48.68 Å2
Refinement stepCycle: LAST / Resolution: 1.8→48.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2357 0 15 169 2541
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052444
X-RAY DIFFRACTIONf_angle_d0.77743305
X-RAY DIFFRACTIONf_chiral_restr0.0532346
X-RAY DIFFRACTIONf_plane_restr0.0053426
X-RAY DIFFRACTIONf_dihedral_angle_d22.17031475
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.850.42881340.42282522X-RAY DIFFRACTION97.08
1.85-1.90.40261420.34752620X-RAY DIFFRACTION100
1.9-1.960.31741560.29862599X-RAY DIFFRACTION99.89
1.96-2.030.27611440.25482608X-RAY DIFFRACTION99.85
2.03-2.120.25921400.222629X-RAY DIFFRACTION100
2.12-2.210.20611380.1852650X-RAY DIFFRACTION100
2.21-2.330.21561520.18752620X-RAY DIFFRACTION99.86
2.33-2.480.23561330.1812643X-RAY DIFFRACTION99.96
2.48-2.670.19731350.18852672X-RAY DIFFRACTION100
2.67-2.930.2511280.18252672X-RAY DIFFRACTION99.96
2.93-3.360.20281340.17332708X-RAY DIFFRACTION99.75
3.36-4.230.17211210.13952737X-RAY DIFFRACTION99.83
4.23-48.040.17711260.16242890X-RAY DIFFRACTION99.74
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
19.377782141753.667206318892.666856473573.85544479891-0.6393766490013.48872110170.251503945068-0.508615279743-0.7554567610180.746682841266-0.1733687374330.4601311853360.540995675159-0.601486465901-0.1827797328070.406825435967-0.07434449218370.002676767096820.305426291383-0.007111768468090.911385330687-6.8118010115711.96312483791.21427084509
25.898429791415.597130078310.193941375969.71898634973-2.926879175896.136470970640.1328321202640.313668352231-0.983824574177-0.09316996105310.001955286968060.08502725647860.920936236646-0.0256664480877-0.1532903325390.3778545969030.0283263169119-0.005990641923390.31927936108-0.176485620530.715242023638-1.907846813639.33032571828-7.36429931093
33.635274094062.476155865763.90856554743.30713721391-0.06453171104669.312990774450.1597711830050.680780275368-0.559519759705-0.754813565813-0.294790590525-0.1159149458740.2140742688560.5176311611910.1230083306360.4349333117980.07706762217610.05284964026530.391123704203-0.08296696213380.57150892289410.487630998216.1880365729-6.22400541757
42.90080937499-0.694202450620.01771143217643.465436292740.2183190390540.9840616851590.0697458719430.324307300166-0.150887792848-0.194725985751-0.008354270434240.327017675629-0.0552675263572-0.1258050903680.0646957973390.263430941267-0.00440196406601-0.03340427483930.284330655479-0.002381730255770.398303703303-11.838597291231.7047808274-1.95814045047
52.907229244041.92251683770.5892835066622.76341449057-0.951973017221.313089304240.2249114136570.444951808765-0.599313931545-0.773663437527-0.2679105056850.634166555787-0.0403688754369-0.595393170447-0.08302198113530.4368466287950.0403333604879-0.07644289231480.471543226839-0.04831767598110.68696742672-18.834256716327.2304373305-4.33222899273
63.30285538343-0.575482181961-0.4213175725293.061567958220.03621601498871.03863640339-0.1223558901820.0223156600764-0.3121448418840.1245303016880.03068173987190.3123117547990.0783297331488-0.112604605850.03833152627580.263844931899-0.01855019928190.001138940567610.2380268227890.00757910175150.393272282942-6.2456265691628.11789609795.32989548538
74.897349875590.242488449775-0.3907437628384.778264236420.3925952330052.359529050250.041270564031.120270666270.234528974431-0.854786150445-0.01382794437180.666672989676-0.326287960906-0.05051802279080.0532350958820.4792865095410.0332180923637-0.03051194886080.4468926589660.01159175270930.505283354938-1.9896227900629.472369709-11.7758500467
84.4852631821-0.0105068896531-0.07273550769113.898234103180.7502219404312.90732327031-0.02456991946660.5205201436020.136435627753-0.616540468917-0.0272081743144-0.374222640334-0.3102351568780.280374141876-0.04940701896510.356221101055-0.009454474266310.03011026249850.3221284831220.0588106162320.3818638106327.6953410133736.0987138075-4.0666880415
94.47310689137-0.584343943780.1025595635373.412491212280.5114806645352.03454101509-0.06180652752750.3014914309-0.122181904032-0.410279832720.0557514347726-0.000790091554816-0.03890353937590.0778474884783-0.0001014721923490.229782958838-0.008379099396010.0137816901770.225793925922-0.0342828505110.3053242827593.0799506624928.0025332266-1.40101303598
107.977501358891.19096888308-1.577268283.63141318456-0.2820867725592.593097544740.0515359182221-0.891017040744-0.4444471942910.745900819229-0.04364156290460.5524436761360.1008593458930.04629881740120.04704684369030.445279191502-0.01045484495020.07974939239510.3414464527020.07723519494270.447038473457-6.724629360728.192874303516.0364697848
113.65731143212-4.040586254540.6597739749276.9776768076-0.1232090184785.18730783994-0.465716777163-0.0780507249570.5420274912190.694384081820.250290161255-0.5464495567880.0860924429112-0.3159388420830.1527089671310.315498738753-0.0983110592982-0.08316361501650.3806145143350.02131792109530.4844405915855.2650678716934.56691974948.34906122829
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'L' and (resid 290 through 299 )
2X-RAY DIFFRACTION2chain 'L' and (resid 300 through 308 )
3X-RAY DIFFRACTION3chain 'L' and (resid 309 through 319 )
4X-RAY DIFFRACTION4chain 'H' and (resid 321 through 375 )
5X-RAY DIFFRACTION5chain 'H' and (resid 376 through 396 )
6X-RAY DIFFRACTION6chain 'H' and (resid 397 through 460 )
7X-RAY DIFFRACTION7chain 'H' and (resid 461 through 489 )
8X-RAY DIFFRACTION8chain 'H' and (resid 490 through 527 )
9X-RAY DIFFRACTION9chain 'H' and (resid 528 through 563 )
10X-RAY DIFFRACTION10chain 'H' and (resid 564 through 579 )
11X-RAY DIFFRACTION11chain 'I' and (resid 1 through 31 )

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