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

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Basic information

Entry
Database: PDB / ID: 6tkj
TitleTsetse thrombin inhibitor in complex with human alpha-thrombin - tetragonal form at 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 / thrombospondin receptor activity / Defective factor XII causes hereditary angioedema / thrombin / thrombin-activated receptor signaling pathway / negative regulation of astrocyte differentiation / regulation of blood coagulation / positive regulation of phospholipase C-activating G protein-coupled receptor signaling pathway / neutrophil-mediated killing of gram-negative bacterium / Defective F8 cleavage by thrombin ...cytolysis by host of symbiont cells / thrombospondin receptor activity / Defective factor XII causes hereditary angioedema / thrombin / thrombin-activated receptor signaling pathway / negative regulation of astrocyte differentiation / regulation of blood coagulation / positive regulation of phospholipase C-activating G protein-coupled receptor signaling pathway / neutrophil-mediated killing of gram-negative bacterium / Defective F8 cleavage by thrombin / Platelet Aggregation (Plug Formation) / ligand-gated ion channel signaling pathway / 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 / Transport of gamma-carboxylated protein precursors from the endoplasmic reticulum to the Golgi apparatus / regulation of cytosolic calcium ion concentration / Gamma-carboxylation of protein precursors / Common Pathway of Fibrin Clot Formation / Removal of aminoterminal propeptides from gamma-carboxylated proteins / fibrinolysis / Intrinsic Pathway of Fibrin Clot Formation / negative regulation of proteolysis / negative regulation of cytokine production involved in inflammatory response / Peptide ligand-binding receptors / Regulation of Complement cascade / positive regulation of release of sequestered calcium ion into cytosol / acute-phase response / Cell surface interactions at the vascular wall / positive regulation of receptor signaling pathway via JAK-STAT / growth factor activity / lipopolysaccharide binding / serine-type endopeptidase inhibitor activity / positive regulation of insulin secretion / platelet activation / response to wounding / positive regulation of protein localization to nucleus / Golgi lumen / 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 / antimicrobial humoral immune response mediated by antimicrobial peptide / regulation of cell shape / heparin binding / : / Thrombin signalling through proteinase activated receptors (PARs) / positive regulation of cell growth / blood microparticle / G alpha (q) signalling events / cell surface receptor signaling pathway / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / 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: 2.81 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 20, 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)40,0614
Polymers39,8403
Non-polymers2211
Water36020
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5150 Å2
ΔGint-12 kcal/mol
Surface area13140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.977, 114.977, 62.512
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

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Components

#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
#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
#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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 20 / Source method: isolated from a natural source / Formula: H2O
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: 3.06 Å3/Da / Density % sol: 59.9 %
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: ID23-1 / Wavelength: 1.771 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 2, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.771 Å / Relative weight: 1
ReflectionResolution: 2.81→81.3 Å / Num. obs: 10690 / % possible obs: 99.5 % / Redundancy: 24.3 % / Biso Wilson estimate: 77.29 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.093 / Net I/σ(I): 28.1
Reflection shellResolution: 2.81→2.96 Å / Redundancy: 23.4 % / Rmerge(I) obs: 1.138 / Mean I/σ(I) obs: 3.7 / Num. unique obs: 1479 / CC1/2: 0.905 / % possible all: 96.8

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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: 2.81→49.56 Å / SU ML: 0.3056 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.436
RfactorNum. reflection% reflection
Rfree0.2441 555 5.21 %
Rwork0.1701 --
obs0.174 10647 99.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 81.42 Å2
Refinement stepCycle: LAST / Resolution: 2.81→49.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2407 0 14 20 2441
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00972479
X-RAY DIFFRACTIONf_angle_d1.33933349
X-RAY DIFFRACTIONf_chiral_restr0.0729349
X-RAY DIFFRACTIONf_plane_restr0.0084431
X-RAY DIFFRACTIONf_dihedral_angle_d23.08811498
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.81-3.090.32561180.24172432X-RAY DIFFRACTION97.85
3.09-3.540.27721370.20812496X-RAY DIFFRACTION100
3.54-4.460.22271450.15182514X-RAY DIFFRACTION100
4.46-49.560.23531550.15782650X-RAY DIFFRACTION99.96
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)
10.6308180600330.02325440984280.09826856900340.603635322075-0.02877802967490.00841239207109-2.103848206151.28442716828-0.579096173752-0.9903227528160.630855749932-0.5182788275740.211561009213-1.731155847980.2701746791651.548931443890.1817124448670.3479939445621.102832073720.1313597426040.925009216011-6.3020033561-15.11603534844.31932572544
23.89412762153-1.28061967494-0.6228261099274.60868381444-1.240225615680.760604694725-0.0277919382804-0.2213069066730.577216364395-0.311910234131-0.708725803204-0.952836909418-0.2714337936770.4690927692640.1654635629980.8987919272270.2091531674310.2834372722350.6249009196790.135673731131.17072352741-4.20445495003-13.33309400514.8335702779
36.577351413140.359866958613-3.349469159736.71581412055-2.662623017415.206890717880.242782110377-1.435116524990.8409419087440.761442437346-0.707471293884-0.0856926009643-1.59645745449-0.002944342985340.04505329189011.119329555750.2811952349460.1755984842940.840827135511-0.01557373960640.888899433572-4.32478828883-9.1515047467420.0575171524
43.8839908677-4.110993577840.7343067205637.24454067543-0.1499335498440.35740806109-0.121546665222-0.03666051216910.5182425214530.419263250241.11502363501-1.241811663230.166054652171-0.2130859065280.1776214064031.0435031953-0.1437902861550.1253369735430.819384293604-0.09178519083950.9163712697181.77174491636-12.165999021625.4338605487
55.66186253785-2.43170954886-1.019087929513.943031617511.592190783122.17799231311.53767597854-1.933399749870.1736066256130.234331591362-0.7562845508191.7439184842-1.499129545390.9562442733070.05866093482590.637322232686-0.1225050265550.07178132243180.8131696922410.05259139923550.49178711428111.7142046227-17.339342296621.8453964717
63.41963341565-0.226419577899-0.6052183598775.18741097426-0.03823066088174.175303067520.194021235175-1.0469515349-0.3493838881760.9660913282580.3905177244280.29078296956-0.6249729285340.144014396334-0.01387557084960.773218732042-0.01839400190850.2034539223990.6565507959450.02577134143130.776767455844-3.66127186772-22.625999921725.971921215
74.603327288621.47962636889-0.8465648906224.74716717113-0.7226626328122.794228166620.3100537427920.0246955950787-0.2894029341320.361562497814-0.3691508955510.1510147366970.251074269369-0.0392741633941-0.1296502283890.6020889412560.1262866961260.06324040562750.8009298673670.07221660990440.788401587416-15.3274106178-30.873848793216.5123493022
83.42193722933-0.0734786914589-0.1808223301434.869103627831.267164840891.62647383772-0.0420189490217-0.1380736163610.133699682140.2531122578540.1081577534890.8368599138330.0542349401233-0.293201411792-0.03515489793190.6653755450720.02239374254410.01992712861460.7246255837150.07188553765350.851968791105-15.3876788568-32.975365537417.1443074451
93.720808079130.663091895573-1.366385626813.976571792380.1405517537431.387954455590.05757899847280.7868354943530.177588701824-0.577274844340.01316627185550.3532069173760.0794495345894-0.472331521306-0.06408300671520.6209209478430.03623566949340.00142479420780.5965284775280.04304009574330.520072591819-8.41102152999-38.34266402796.90388566114
104.534739194871.060137028960.100555615143.404653136430.1812929961091.927872925570.05829235301970.1029237727991.0248519389-0.17693568434-0.02448265936710.324537491568-0.44328802963-0.240473841008-0.08275062363750.5388717278380.06350319215980.03301388936110.4709360179830.08049988940570.596967938117-2.98404832216-22.268069000211.6399154765
113.392000897410.148623849629-2.265155922363.28851806437-0.2359412140532.37861435563-0.251720157844-0.911961435533-0.2363062448180.3516263134370.1983230841680.3603473809160.524951898151-0.0328096962592-0.01823990011090.621030063765-0.0538369639616-0.05109216906260.779939579620.2033019872620.691196046597-0.996207621627-31.075665316626.7720213563
125.678738469622.424750034811.385636348774.119664933121.235027671892.40480490164-0.09759067825280.349747455097-0.574435015845-0.2142201142560.33709144295-1.080585356140.5083264614431.01506981538-0.00468118845370.7222349779190.1213819621720.1093364547150.7670011736420.03017554197670.77237888807511.3618130026-42.305726743612.7120359631
134.093096161830.7070116877430.6591069771823.230660321750.9739793863394.825259817640.0821707277591-0.915734340759-0.7394929045570.134794395908-0.14541822064-0.3652149916210.8112193420390.0859922830948-0.06187226139980.568818767436-0.0197273976008-0.01030922556280.7611759841350.1911254679610.5528878727856.43079970089-34.044237927723.6122999113
143.55163207398-0.406649279022-0.3638223343692.732291251120.2375188721882.28033127116-0.0197535616503-0.3160478975750.08790081393990.8482899696990.00569189427311-0.541318369816-0.233558096810.0660318161944-0.06868576391240.5553904871120.015277085019-0.02386507926770.6270294586470.01994200004750.7183861620764.18182468647-28.325576444317.2894046586
154.53522289319-0.2355779192210.3630237144844.14928267666-1.446495152514.221640628990.2366947159880.9190150139-0.0724981001885-0.7503876504080.0373379725017-0.1705302290590.9105248205520.661169594498-0.05062278097790.6715247162370.0634945326131-0.008165742490070.6049880774390.04967115134610.371163791704-2.00100699456-30.68647174022.84885252427
161.88595167741.323997329390.2096007139682.6528348028-1.137172374363.04439566393-0.6056973691010.205636058749-0.149768175513-0.6610552352920.0140416536581-0.719426908317-0.293294863841-1.022686244890.2760091579420.6189256193190.08517849945630.1662565341040.926518494606-0.09693150406330.8445434824986.01446213972-35.90990887676.71476803454
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'L' and (resid 288 through 292 )
2X-RAY DIFFRACTION2chain 'L' and (resid 293 through 297 )
3X-RAY DIFFRACTION3chain 'L' and (resid 298 through 302 )
4X-RAY DIFFRACTION4chain 'L' and (resid 303 through 308 )
5X-RAY DIFFRACTION5chain 'L' and (resid 309 through 318 )
6X-RAY DIFFRACTION6chain 'H' and (resid 321 through 334 )
7X-RAY DIFFRACTION7chain 'H' and (resid 335 through 356 )
8X-RAY DIFFRACTION8chain 'H' and (resid 357 through 396 )
9X-RAY DIFFRACTION9chain 'H' and (resid 397 through 420 )
10X-RAY DIFFRACTION10chain 'H' and (resid 421 through 460 )
11X-RAY DIFFRACTION11chain 'H' and (resid 461 through 489 )
12X-RAY DIFFRACTION12chain 'H' and (resid 490 through 504 )
13X-RAY DIFFRACTION13chain 'H' and (resid 505 through 527 )
14X-RAY DIFFRACTION14chain 'H' and (resid 528 through 557 )
15X-RAY DIFFRACTION15chain 'H' and (resid 558 through 577 )
16X-RAY DIFFRACTION16chain 'I' and (resid 1 through 31 )

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