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- PDB-3pb1: Crystal Structure of a Michaelis Complex between Plasminogen Acti... -

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Basic information

Entry
Database: PDB / ID: 3pb1
TitleCrystal Structure of a Michaelis Complex between Plasminogen Activator Inhibitor-1 and Urokinase-type Plasminogen Activator
Components
  • Plasminogen activator inhibitor 1
  • Plasminogen activator, urokinase
Keywordshydrolase Inhibitor/Hydrolase / PAI-1 / uPA / Michaelis complex / Structural Genomics / Structure 2 Function Project / S2F / hydrolase Inhibitor-Hydrolase complex
Function / homology
Function and homology information


positive regulation of leukotriene production involved in inflammatory response / dentinogenesis / negative regulation of smooth muscle cell-matrix adhesion / 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 / u-plasminogen activator ...positive regulation of leukotriene production involved in inflammatory response / dentinogenesis / negative regulation of smooth muscle cell-matrix adhesion / 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 / u-plasminogen activator / regulation of smooth muscle cell-matrix adhesion / negative regulation of blood coagulation / urokinase plasminogen activator signaling pathway / regulation of plasminogen activation / regulation of fibrinolysis / negative regulation of endopeptidase activity / regulation of wound healing / protein complex involved in cell-matrix adhesion / negative regulation of plasminogen activation / regulation of smooth muscle cell migration / regulation of signaling receptor activity / serine-type endopeptidase complex / Dissolution of Fibrin Clot / positive regulation of monocyte chemotaxis / smooth muscle cell migration / plasminogen activation / tertiary granule membrane / regulation of cell adhesion mediated by integrin / replicative senescence / ECM proteoglycans / positive regulation of blood coagulation / negative regulation of fibrinolysis / specific granule membrane / negative regulation of endothelial cell apoptotic process / regulation of cell adhesion / 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 / positive regulation of interleukin-8 production / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / serine-type endopeptidase inhibitor activity / positive regulation of inflammatory response / positive regulation of receptor-mediated endocytosis / positive regulation of angiogenesis / chemotaxis / blood coagulation / Platelet degranulation / regulation of cell population proliferation / collagen-containing extracellular matrix / angiogenesis / cellular response to lipopolysaccharide / protease binding / defense response to Gram-negative bacterium / response to hypoxia / positive regulation of cell migration / external side of plasma membrane / signaling receptor binding / serine-type endopeptidase activity / focal adhesion / Neutrophil degranulation / cell surface / signal transduction / proteolysis / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
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 ...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 / 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 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
Urokinase-type plasminogen activator / Plasminogen activator inhibitor 1 / :
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsLin, Z. / Jiang, L. / Huang, M. / Structure 2 Function Project (S2F)
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Structural basis for recognition of urokinase-type plasminogen activator by plasminogen activator inhibitor-1.
Authors: Lin, Z. / Jiang, L. / Yuan, C. / Jensen, J.K. / Zhang, X. / Luo, Z. / Furie, B.C. / Furie, B. / Andreasen, P.A. / Huang, M.
History
DepositionOct 20, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 29, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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: Plasminogen activator, urokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,4144
Polymers71,2212
Non-polymers1922
Water5,657314
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2120 Å2
ΔGint-4 kcal/mol
Surface area25590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.711, 97.711, 171.916
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

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


Mass: 42795.066 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 Plasminogen activator, urokinase /


Mass: 28426.373 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 143-395 / Mutation: S195A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PLAU, RP11-417O11.1-002 / Production host: Pichia pastoris (fungus)
References: UniProt: Q5SWW8, UniProt: P00749*PLUS, u-plasminogen activator
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 314 / 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: 3.33 Å3/Da / Density % sol: 63.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 1.4M ammonium sulfate, 0.1M Tris-HCl, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1 Å
DetectorDetector: DIFFRACTOMETER / Date: Jun 16, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→99 Å / Num. all: 81438 / Num. obs: 80462 / % possible obs: 99.9 % / Redundancy: 5.9 % / Rmerge(I) obs: 0.162 / Rsym value: 0.185 / Net I/σ(I): 21.5
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.589 / Mean I/σ(I) obs: 3.4 / Num. unique all: 3996 / Rsym value: 0.633 / % possible all: 98.5

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Processing

Software
NameVersionClassification
HKL-2000data collection
CCP4model building
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1DVM

1dvm


Resolution: 2.3→38.32 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.891 / SU B: 6.525 / SU ML: 0.16 / Cross valid method: THROUGHOUT / ESU R Free: 0.23 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27199 2142 5 %RANDOM
Rwork0.22049 ---
obs0.22304 40338 99.11 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.466 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.3→38.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4926 0 10 314 5250
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0225061
X-RAY DIFFRACTIONr_angle_refined_deg1.261.956864
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.725619
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.97723.6225
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.95815862
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.6171531
X-RAY DIFFRACTIONr_chiral_restr0.0910.2760
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213804
X-RAY DIFFRACTIONr_mcbond_it0.5861.53098
X-RAY DIFFRACTIONr_mcangle_it1.1425025
X-RAY DIFFRACTIONr_scbond_it1.56231963
X-RAY DIFFRACTIONr_scangle_it2.724.51839
LS refinement shellResolution: 2.301→2.361 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.325 164 -
Rwork0.249 2885 -
obs--98.55 %

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