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- PDB-6zrv: Crystal Structure of Stabilized Active Plasminogen Activator Inhi... -

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Basic information

Entry
Database: PDB / ID: 6zrv
TitleCrystal Structure of Stabilized Active Plasminogen Activator Inhibitor-1 (PAI-1-W175F) in Complex with an Inhibitory Nanobody (VHH-s-a93, Nb93)
Components
  • Plasminogen activator inhibitor 1
  • VHH-s-a93 (Nb93)
KeywordsHYDROLASE / plasminogen activator inhibitor-1 / PAI-1 / PAI-1-W175F / serpin / serine protease inhibitor / nanobody / antibody fragment / protein 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 / negative regulation of endopeptidase activity ...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 / 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 / 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 / positive regulation of interleukin-8 production / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / serine-type endopeptidase inhibitor activity / positive regulation of receptor-mediated endocytosis / positive regulation of inflammatory response / positive regulation of angiogenesis / Platelet degranulation / cellular response to lipopolysaccharide / angiogenesis / collagen-containing extracellular matrix / defense response to Gram-negative bacterium / protease binding / signaling receptor binding / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
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
Similarity search - Domain/homology
Plasminogen activator inhibitor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Vicugna pacos (alpaca)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 Å
AuthorsSillen, M. / Weeks, S.D. / Strelkov, S.V. / Declerck, P.J.
Funding support Belgium, 2items
OrganizationGrant numberCountry
Research Foundation - Flanders (FWO)G072915N Belgium
Research Foundation - Flanders (FWO)11ZQ918N Belgium
CitationJournal: Int J Mol Sci / Year: 2020
Title: Structural Insights into the Mechanism of a Nanobody That Stabilizes PAI-1 and Modulates Its Activity.
Authors: Sillen, M. / Weeks, S.D. / Strelkov, S.V. / Declerck, P.J.
History
DepositionJul 15, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 26, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 2, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed ..._citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jan 31, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Plasminogen activator inhibitor 1
B: VHH-s-a93 (Nb93)


Theoretical massNumber of molelcules
Total (without water)56,0322
Polymers56,0322
Non-polymers00
Water5,675315
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1900 Å2
ΔGint-8 kcal/mol
Surface area20120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.808, 117.808, 96.483
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

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


Mass: 42780.031 Da / Num. of mol.: 1 / Mutation: W175F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SERPINE1, PAI1, PLANH1 / Plasmid: pETHSUK2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta 2(DE3)pLysS / References: UniProt: P05121
#2: Antibody VHH-s-a93 (Nb93)


Mass: 13252.426 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vicugna pacos (alpaca) / Plasmid: pETHSUK2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta 2(DE3)pLysS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 315 / 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: 2.99 Å3/Da / Density % sol: 58.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 1 M DIAMMONIUM PHOSPHATE, O.1 M TRISODIUM CITRATE, 0.2 M SODIUM CHLORIDE

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.978934 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 2, 2018
RadiationMonochromator: Si (111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978934 Å / Relative weight: 1
ReflectionResolution: 1.78→83.3 Å / Num. obs: 65134 / % possible obs: 100 % / Redundancy: 13 % / CC1/2: 0.998 / Rmerge(I) obs: 0.126 / Rpim(I) all: 0.036 / Rrim(I) all: 0.131 / Net I/σ(I): 10.9
Reflection shellResolution: 1.78→1.88 Å / Redundancy: 12.8 % / Rmerge(I) obs: 2.042 / Num. unique obs: 9357 / CC1/2: 0.697 / Rpim(I) all: 0.589 / Rrim(I) all: 2.127 / % possible all: 100

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Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3Q02, 5TP3

3q02

5tp3


Resolution: 1.88→52.69 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 24.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2328 2315 4.16 %
Rwork0.1965 53326 -
obs0.1979 55641 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 83.08 Å2 / Biso mean: 36.6323 Å2 / Biso min: 19.24 Å2
Refinement stepCycle: final / Resolution: 1.88→52.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3783 0 0 315 4098
Biso mean---41.16 -
Num. residues----494
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 17 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.88-1.920.32811420.285130803222
1.92-1.960.30681450.25630863231
1.96-2.010.3071190.240731163235
2.01-2.060.28021460.223930763222
2.06-2.110.21621250.212330923217
2.11-2.170.24761450.200830843229
2.17-2.240.27941490.206330923241
2.24-2.320.23111340.203730913225
2.32-2.420.25751400.211431373277
2.42-2.530.27171180.216531203238
2.53-2.660.25141370.219531083245
2.66-2.830.26181170.216931733290
2.83-3.050.24831400.21931333273
3.05-3.350.23521430.211831453288
3.35-3.840.20031310.174631843315
3.84-4.830.20251380.153432223360
4.83-52.690.20591460.186433873533

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