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- PDB-5gim: Crystal structure of thrombin-avathrin complex -

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Basic information

Entry
Database: PDB / ID: 5gim
TitleCrystal structure of thrombin-avathrin complex
Components
  • C-terminal peptide from Putative uncharacterized protein avahiru
  • N-terminal peptide from Putative uncharacterized protein avahiru
  • Thrombin light chain
  • thrombin heavy chain
Keywordshydrolase/hydrolase inhibitor / hydrolase / hydrolase-hydrolase inhibitor 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 / 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 / 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
Prothrombin / Uncharacterized protein avahiru
Similarity search - Component
Biological speciesHomo sapiens (human)
Amblyomma variegatum (tropical bont tick)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.09 Å
AuthorsKini, R.M. / Koh, C.Y. / Iyer, J.K. / Swaminathan, K.
Funding support Singapore, 1items
OrganizationGrant numberCountry
Singapore
CitationJournal: FASEB J. / Year: 2017
Title: Avathrin: a novel thrombin inhibitor derived from a multicopy precursor in the salivary glands of the ixodid tick, Amblyomma variegatum.
Authors: Iyer, J.K. / Koh, C.Y. / Kazimirova, M. / Roller, L. / Jobichen, C. / Swaminathan, K. / Mizuguchi, J. / Iwanaga, S. / Nuttall, P.A. / Chan, M.Y. / Kini, R.M.
History
DepositionJun 24, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 3, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 12, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Nov 8, 2023Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Thrombin light chain
B: thrombin heavy chain
C: N-terminal peptide from Putative uncharacterized protein avahiru
D: C-terminal peptide from Putative uncharacterized protein avahiru


Theoretical massNumber of molelcules
Total (without water)37,0374
Polymers37,0374
Non-polymers00
Water3,333185
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4170 Å2
ΔGint-22 kcal/mol
Surface area13210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.470, 71.580, 71.720
Angle α, β, γ (deg.)90.000, 99.860, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein/peptide Thrombin light chain


Mass: 4096.534 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: F2 / Plasmid: pCAGG / Cell line (production host): Sp2/0-Ag14 / Production host: Mus musculus (house mouse) / References: UniProt: P00734, thrombin
#2: Protein thrombin heavy chain


Mass: 29780.219 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: F2 / Cell line (production host): Sp2/0-Ag14 / Production host: Mus musculus (house mouse) / References: thrombin
#3: Protein/peptide N-terminal peptide from Putative uncharacterized protein avahiru


Mass: 983.079 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: solid phase peptide synthesis / Source: (synth.) Amblyomma variegatum (tropical bont tick) / References: UniProt: Q6F3E8, UniProt: P00734*PLUS
#4: Protein/peptide C-terminal peptide from Putative uncharacterized protein avahiru


Mass: 2177.343 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: solid phase peptide synthesis / Source: (synth.) Amblyomma variegatum (tropical bont tick) / References: UniProt: Q6F3E8
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 185 / 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: 2.37 Å3/Da / Density % sol: 48.14 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.4 / Details: 0.1M HEPES, 20-25% PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5419 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Aug 17, 2015
RadiationMonochromator: VariMax HF (Osmic) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5419 Å / Relative weight: 1
ReflectionResolution: 2.09→70.66 Å / Num. obs: 19156 / % possible obs: 92.7 % / Redundancy: 3.8 % / CC1/2: 0.997 / Rmerge(I) obs: 0.052 / Net I/σ(I): 16.5
Reflection shellResolution: 2.09→2.15 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.137 / % possible all: 82.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.09 Å31.93 Å
Translation2.09 Å31.93 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
MOSFLMdata collection
Aimless0.3.11data scaling
PHASER2.5.6phasing
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2HGT

2hgt


Resolution: 2.09→70.66 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.935 / Matrix type: sparse / SU B: 8.119 / SU ML: 0.118 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.228 / ESU R Free: 0.178
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2159 941 4.9 %RANDOM
Rwork0.1792 ---
obs0.181 18213 92.34 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 80.09 Å2 / Biso mean: 25.098 Å2 / Biso min: 7.48 Å2
Baniso -1Baniso -2Baniso -3
1-1.11 Å20 Å2-0.6 Å2
2---0.45 Å20 Å2
3----0.42 Å2
Refinement stepCycle: final / Resolution: 2.09→70.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2388 0 0 185 2573
Biso mean---26.1 -
Num. residues----298
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0192506
X-RAY DIFFRACTIONr_bond_other_d0.0020.022385
X-RAY DIFFRACTIONr_angle_refined_deg1.3231.9613389
X-RAY DIFFRACTIONr_angle_other_deg0.90635500
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4695305
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.13923.193119
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.4515448
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4711523
X-RAY DIFFRACTIONr_chiral_restr0.0810.2352
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212812
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02585
X-RAY DIFFRACTIONr_mcbond_it0.2230.9651211
X-RAY DIFFRACTIONr_mcbond_other0.2230.9651210
X-RAY DIFFRACTIONr_mcangle_it0.4051.4461513
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)WRfactor Rwork
2.085-2.1390.23620.1661157149781.430.166
2.139-2.1980.249770.1851297151590.6930.185
2.198-2.2610.267580.1881255143491.5620.188
2.261-2.3310.243540.1761221139291.5950.176
2.331-2.4070.207620.1691198137891.4370.169
2.407-2.4920.264660.1831169133792.3710.183
2.492-2.5860.221630.1841089124192.8280.184
2.586-2.6910.24550.1961082123292.2890.196
2.691-2.8110.24450.1881053117493.5260.188
2.811-2.9470.233500.1991007113093.540.199
2.947-3.1070.23480.197968107894.2490.197
3.107-3.2950.233400.175904100693.8370.175
3.295-3.5220.211460.18586696194.9010.185
3.522-3.8030.172520.16379288895.0450.163
3.803-4.1650.229390.16274482594.9090.162
4.165-4.6540.165400.13865973495.2320.138
4.654-5.370.178310.15861267095.970.158
5.37-6.5680.265200.19351055096.3640.193
6.568-9.2490.193270.20940144895.5360.209
9.249-70.6610.16660.26423025492.9130.264
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)
117.3072-4.45848.65768.55270.603710.0178-0.3646-1.13720.42920.1810.1780.7288-0.5761-0.64270.18660.1325-0.02510.02830.1069-0.0360.13269.4399.39788.366
22.73230.15621.439719.023210.48268.8793-0.01420.1353-0.0094-0.09690.1502-0.6587-0.22110.5127-0.1360.0683-0.04550.00920.11760.05790.079519.8945.60284.551
315.2732-3.03781.64659.97331.516711.65260.25920.86960.6671-0.3213-0.28450.28960.33930.25190.02520.1311-0.03080.08620.0883-0.00910.134615.918-0.07872.262
43.20821.25170.97451.65460.32821.79460.3211-0.5665-0.27840.3504-0.28550.03490.259-0.2194-0.03560.1214-0.09130.00660.11910.03940.04392.77-7.57296.149
53.61141.24210.71811.40950.06251.84570.0817-0.20340.10560.0021-0.12520.17290.0592-0.31190.04350.0622-0.03350.00950.0718-0.02570.025-0.848-3.65287.214
62.67453.18511.85974.3332.69725.4224-0.1317-0.0343-0.2763-0.1885-0.0324-0.19060.2121-0.2690.1640.1119-0.00570.06360.028-0.00920.10256.201-14.43778.061
72.69191.43180.31833.1043-0.15322.083-0.01720.1789-0.1448-0.1628-0.02890.0130.1788-0.14960.04610.0615-0.0240.00170.0428-0.02170.01412.482-6.41679.419
85.99348.14669.360614.656110.191616.42610.19310.0266-0.4321-0.36590.0956-1.03050.7348-0.0473-0.28870.3603-0.0251-0.03350.4508-0.04670.4848-2.787-20.51382.281
916.2168-0.10860.94414.51075.50713.11650.0495-0.25710.65030.137-0.05370.5167-0.1116-0.42590.00410.2311-0.14320.00030.43630.13880.2065.658-7.136109.198
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1E - 7
2X-RAY DIFFRACTION2A8 - 14D
3X-RAY DIFFRACTION3A14E - 14K
4X-RAY DIFFRACTION4B16 - 80
5X-RAY DIFFRACTION5B81 - 147
6X-RAY DIFFRACTION6B149E - 176
7X-RAY DIFFRACTION7B177 - 246
8X-RAY DIFFRACTION8C5 - 10
9X-RAY DIFFRACTION9D19 - 28

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