6GWQ

Crystal Structure of Stabilized Active Plasminogen Activator Inhibitor-1 (PAI-1-stab) in Complex with an Inhibitory Nanobody (VHH-2g-42)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.32 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.207 

Starting Models: experimental
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This is version 1.3 of the entry. See complete history


Literature

Molecular mechanism of two nanobodies that inhibit PAI-1 activity reveals a modulation at distinct stages of the PAI-1/plasminogen activator interaction.

Sillen, M.Weeks, S.D.Zhou, X.Komissarov, A.A.Florova, G.Idell, S.Strelkov, S.V.Declerck, P.J.

(2020) J Thromb Haemost 18: 681-692

  • DOI: https://doi.org/10.1111/jth.14716
  • Primary Citation of Related Structures:  
    6GWN, 6GWP, 6GWQ

  • PubMed Abstract: 

    Plasminogen activator inhibitor-1 (PAI-1), a key inhibitor of plasminogen activators (PAs) tissue-type PA (tPA) and urokinase-type PA (uPA) plays a crucial role in many (patho)physiological processes (e.g., cardiovascular disease, tissue fibrosis) as well as in many age-related pathologies. Therefore, much effort has been put into the development of small molecule or antibody-based PAI-1 inhibitors. To elucidate the molecular mechanism of nanobody-induced PAI-1 inhibition. Here we present the first crystal structures of PAI-1 in complex with two neutralizing nanobodies (Nbs). These structures, together with biochemical and biophysical characterization, reveal that Nb VHH-2g-42 (Nb42) interferes with the initial PAI-1/PA complex formation, whereas VHH-2w-64 (Nb64) redirects the PAI-1/PA interaction to PAI-1 deactivation and regeneration of active PA. Furthermore, whereas vitronectin does not have an impact on the inhibitory effect of Nb42, it strongly potentiates the inhibitory effect of Nb64, which may contribute to a strong inhibitory potential of Nb64 in vivo. These findings illuminate the molecular mechanisms of PAI-1 inhibition. Nb42 and Nb64 can be used as starting points to engineer further improved antibody-based PAI-1 inhibitors or guide the rational design of small molecule inhibitors to treat a wide range of PAI-1-related pathophysiological conditions.


  • Organizational Affiliation

    Laboratory for Therapeutic and Diagnostic Antibodies, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Leuven, Belgium.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Plasminogen Activator Inhibitor-1379Homo sapiensMutation(s): 5 
Gene Names: SERPINE1
UniProt & NIH Common Fund Data Resources
Find proteins for P05121 (Homo sapiens)
Explore P05121 
Go to UniProtKB:  P05121
PHAROS:  P05121
GTEx:  ENSG00000106366 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP05121
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
VHH-2g-42116Vicugna pacosMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.32 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.207 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 89.87α = 90
b = 123.647β = 129.94
c = 64.975γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Research Foundation - FlandersBelgiumG072915N
Research Foundation - FlandersBelgium11ZQ916N

Revision History  (Full details and data files)

  • Version 1.0: 2020-01-01
    Type: Initial release
  • Version 1.1: 2020-03-11
    Changes: Database references
  • Version 1.2: 2021-02-10
    Changes: Derived calculations
  • Version 1.3: 2024-01-17
    Changes: Data collection, Database references, Refinement description