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- PDB-5brr: Michaelis complex of tPA-S195A:PAI-1 -

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Basic information

Entry
Database: PDB / ID: 5brr
TitleMichaelis complex of tPA-S195A:PAI-1
Components
  • Plasminogen activator inhibitor 1
  • Tissue-type plasminogen activator
KeywordsHYDROLASE INHIBITOR/HYDROLASE / Tissue-Type Plasminogen Activator Catalytic Domain / Plasminogen Activator Inhibitor 1 / Structure-Activity Relationship / Thrombolysis / HYDROLASE INHIBITOR-HYDROLASE complex
Function / homology
Function and homology information


t-plasminogen activator / positive regulation of leukotriene production involved in inflammatory response / prevention of polyspermy / dentinogenesis / negative regulation of smooth muscle cell-matrix adhesion / trans-synaptic signaling by BDNF, modulating synaptic transmission / negative regulation of smooth muscle cell migration / peptidase inhibitor complex / negative regulation of vascular wound healing / negative regulation of wound healing ...t-plasminogen activator / positive regulation of leukotriene production involved in inflammatory response / prevention of polyspermy / dentinogenesis / negative regulation of smooth muscle cell-matrix adhesion / trans-synaptic signaling by BDNF, modulating synaptic transmission / negative regulation of smooth muscle cell migration / peptidase inhibitor complex / negative regulation of vascular wound healing / negative regulation of wound healing / positive regulation of odontoblast differentiation / negative regulation of cell adhesion mediated by integrin / Signaling by PDGF / negative regulation of endopeptidase activity / negative regulation of plasminogen activation / negative regulation of blood coagulation / regulation of signaling receptor activity / positive regulation of monocyte chemotaxis / Dissolution of Fibrin Clot / smooth muscle cell migration / plasminogen activation / platelet-derived growth factor receptor signaling pathway / replicative senescence / ECM proteoglycans / positive regulation of blood coagulation / negative regulation of fibrinolysis / negative regulation of endothelial cell apoptotic process / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / serine protease inhibitor complex / fibrinolysis / negative regulation of cell migration / BMAL1:CLOCK,NPAS2 activates circadian gene expression / platelet alpha granule lumen / secretory granule / positive regulation of interleukin-8 production / negative regulation of proteolysis / phosphoprotein binding / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / Schaffer collateral - CA1 synapse / serine-type endopeptidase inhibitor activity / protein modification process / positive regulation of receptor-mediated endocytosis / positive regulation of inflammatory response / positive regulation of angiogenesis / blood coagulation / Platelet degranulation / apical part of cell / cellular response to lipopolysaccharide / angiogenesis / collagen-containing extracellular matrix / defense response to Gram-negative bacterium / protease binding / response to hypoxia / serine-type endopeptidase activity / signaling receptor binding / glutamatergic synapse / cell surface / proteolysis / extracellular space / extracellular exosome / extracellular region / plasma membrane / cytoplasm
Similarity search - Function
Tissue plasminogen activator / Fibronectin type I domain / Fibronectin, type I / Fibronectin type-I domain signature. / Fibronectin type-I domain profile. / Fibronectin type 1 domain / Antithrombin; Chain I, domain 2 / Antithrombin, subunit I, domain 2 / Alpha-1-antitrypsin; domain 1 / Alpha-1-antitrypsin, domain 1 ...Tissue plasminogen activator / Fibronectin type I domain / Fibronectin, type I / Fibronectin type-I domain signature. / Fibronectin type-I domain profile. / Fibronectin type 1 domain / Antithrombin; Chain I, domain 2 / Antithrombin, subunit I, domain 2 / Alpha-1-antitrypsin; domain 1 / Alpha-1-antitrypsin, domain 1 / Serpin, conserved site / Serpins signature. / Serpin superfamily, domain 2 / Serpin family / Serpin domain / Serpin superfamily / Serpin superfamily, domain 1 / Serpin (serine protease inhibitor) / SERine Proteinase INhibitors / EGF-like domain / Kringle domain / Kringle / Kringle, conserved site / Kringle superfamily / Kringle domain signature. / Kringle domain profile. / Kringle domain / Kringle-like fold / EGF-like domain profile. / EGF-like domain signature 2. / EGF-like domain signature 1. / EGF-like domain / 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 / Roll / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
TRIETHYLENE GLYCOL / Tissue-type plasminogen activator / Plasminogen activator inhibitor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.16 Å
AuthorsGong, L.
Funding support China, 3items
OrganizationGrant numberCountry
National Natural Science Foundation of China31170707 China
National Natural Science Foundation of China31370737 China
CAS/SFEA International Partnership Program for Creative Research Teams China
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Crystal Structure of the Michaelis Complex between Tissue-type Plasminogen Activator and Plasminogen Activators Inhibitor-1
Authors: Gong, L. / Liu, M. / Zeng, T. / Shi, X. / Yuan, C. / Andreasen, P.A. / Huang, M.
History
DepositionJun 1, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 2, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 9, 2015Group: Database references
Revision 1.2Sep 16, 2015Group: Database references
Revision 1.3Nov 11, 2015Group: Database references
Revision 1.4Oct 18, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
I: Plasminogen activator inhibitor 1
E: Tissue-type plasminogen activator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,4247
Polymers70,9062
Non-polymers5195
Water64936
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3150 Å2
ΔGint-4 kcal/mol
Surface area25370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.740, 73.940, 201.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Plasminogen activator inhibitor 1 / PAI-1 / Endothelial plasminogen activator inhibitor / Serpin E1


Mass: 42782.023 Da / Num. of mol.: 1 / Mutation: N150H, K154T, Q319L, M354I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SERPINE1, PAI1, PLANH1 / Production host: Escherichia coli (E. coli) / References: UniProt: P05121
#2: Protein Tissue-type plasminogen activator / tPA


Mass: 28123.844 Da / Num. of mol.: 1 / Fragment: UNP residues 311-562 / Mutation: C120A, N173Q, S203A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PLAT / Production host: Komagataella pastoris CBS 7435 (fungus) / Strain (production host): X-33 / References: UniProt: P00750, t-plasminogen activator
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 36 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.62 Å3/Da / Density % sol: 53 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, sitting drop / pH: 7.4 / Details: 8% PEG 6000, 0.1 M Tris-HCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 10, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.16→35.43 Å / Num. obs: 13390 / % possible obs: 99.9 % / Redundancy: 6.9 % / Net I/σ(I): 6.9
Reflection shellHighest resolution: 3.16 Å / Redundancy: 7.2 % / Mean I/σ(I) obs: 2.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
MOLREPmodel building
HKL-2000data collection
RefinementResolution: 3.16→35.43 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.852 / SU B: 25.619 / SU ML: 0.448 / Cross valid method: FREE R-VALUE / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27596 662 4.9 %RANDOM
Rwork0.20349 ---
obs0.2071 12728 99.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 47.843 Å2
Baniso -1Baniso -2Baniso -3
1--3.55 Å20 Å2-0 Å2
2---2.61 Å20 Å2
3---6.16 Å2
Refinement stepCycle: 1 / Resolution: 3.16→35.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4918 0 34 36 4988
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0195045
X-RAY DIFFRACTIONr_bond_other_d0.0090.024818
X-RAY DIFFRACTIONr_angle_refined_deg1.5221.9556791
X-RAY DIFFRACTIONr_angle_other_deg0.885311061
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6885596
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.47923.636231
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.61115849
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.2291534
X-RAY DIFFRACTIONr_chiral_restr0.0730.2763
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0215515
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021167
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.4374.6632465
X-RAY DIFFRACTIONr_mcbond_other2.4354.6622464
X-RAY DIFFRACTIONr_mcangle_it4.1186.9723034
X-RAY DIFFRACTIONr_mcangle_other4.1186.9733035
X-RAY DIFFRACTIONr_scbond_it2.1944.9322580
X-RAY DIFFRACTIONr_scbond_other2.1934.9322580
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.737.2913758
X-RAY DIFFRACTIONr_long_range_B_refined7.13537.7275905
X-RAY DIFFRACTIONr_long_range_B_other7.13537.7295906
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.16→3.242 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.312 59 -
Rwork0.238 893 -
obs--99.79 %

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