6ZRV | pdb_00006zrv

Crystal Structure of Stabilized Active Plasminogen Activator Inhibitor-1 (PAI-1-W175F) in Complex with an Inhibitory Nanobody (VHH-s-a93, Nb93)

• PDB DOI: https://doi.org/10.2210/pdb6ZRV/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens, Vicugna pacos
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2020-07-15 Released: 2020-08-26 
• Deposition Author(s): Sillen, M., Weeks, S.D., Strelkov, S.V., Declerck, P.J.
• Funding Organization(s): Research Foundation - Flanders (FWO)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.88 Å
• R-Value Free: 
  0.233 (Depositor), 0.235 (DCC) 
• R-Value Work: 
  0.197 (Depositor), 0.199 (DCC) 
• R-Value Observed: 
  0.198 (Depositor) 

Starting Models: experimental

Literature

Structural Insights into the Mechanism of a Nanobody That Stabilizes PAI-1 and Modulates Its Activity.

Sillen, M., Weeks, S.D., Strelkov, S.V., Declerck, P.J.

(2020) Int J Mol Sci 21

• PubMed: 32824134 
• DOI: https://doi.org/10.3390/ijms21165859
• Primary Citation Related Structures: 
  6ZRV


• PubMed Abstract: 
  

  Plasminogen activator inhibitor-1 (PAI-1) is the main physiological inhibitor of tissue-type (tPA) and urokinase-type (uPA) plasminogen activators (PAs). Apart from being critically involved in fibrinolysis and wound healing, emerging evidence indicates that PAI-1 plays an important role in many diseases, including cardiovascular disease, tissue fibrosis, and cancer. Targeting PAI-1 is therefore a promising therapeutic strategy in PAI-1 related pathologies. Despite ongoing efforts no PAI-1 inhibitors were approved to date for therapeutic use in humans. A better understanding of the molecular mechanisms of PAI-1 inhibition is therefore necessary to guide the rational design of PAI-1 modulators. Here, we present a 1.9 Å crystal structure of PAI-1 in complex with an inhibitory nanobody VHH-s-a93 (Nb93). Structural analysis in combination with biochemical characterization reveals that Nb93 directly interferes with PAI-1/PA complex formation and stabilizes the active conformation of the PAI-1 molecule.

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Organizational Affiliation: 
• Laboratory for Therapeutic and Diagnostic Antibodies, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, B-3000 Leuven, Belgium.
Laboratory for Biocrystallography, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, B-3000 Leuven, Belgium.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: SAXS

Macromolecule Content 

• Total Structure Weight: 56.03 kDa 
• Atom Count: 4,098 
• Modeled Residue Count: 494 
• Deposited Residue Count: 502 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Plasminogen activator inhibitor 1	A	379	Homo sapiens	Mutation(s): 1  Gene Names: SERPINE1, PAI1, PLANH1
UniProt & NIH Common Fund Data Resources
Find proteins for P05121 (Homo sapiens) Explore P05121  Go to UniProtKB:  P05121
PHAROS:  P05121 GTEx:  ENSG00000106366

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
VHH-s-a93 (Nb93)	B	123	Vicugna pacos	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.88 Å
• R-Value Free:  0.233 (Depositor), 0.235 (DCC) 
• R-Value Work:  0.197 (Depositor), 0.199 (DCC) 
• R-Value Observed: 0.198 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 117.808	α = 90
b = 117.808	β = 90
c = 96.483	γ = 90

Software Package:

Software Name	Purpose
Aimless	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2020-08-26 
Deposition Author(s): Sillen, M., Weeks, S.D., Strelkov, S.V., Declerck, P.J.

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Funding Organization	Location	Grant Number
Research Foundation - Flanders (FWO)	Belgium	G072915N
Research Foundation - Flanders (FWO)	Belgium	11ZQ918N

Revision History  

• Version 1.0: 2020-08-26
  Type: Initial release
  
• Version 1.1: 2020-09-02
  Changes: Database references
• Version 1.2: 2024-01-31
  Changes: Data collection, Database references, Refinement description
• Version 1.3: 2024-10-16
  Changes: Structure summary