6GWN

Crystal Structure of Stabilized Active Plasminogen Activator Inhibitor-1 (PAI-1-W175F) in Complex with Two Inhibitory Nanobodies (VHH-2g-42, VHH-2w-64)

• PDB DOI: https://doi.org/10.2210/pdb6GWN/pdb

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


• Deposited: 2018-06-25 Released: 2020-01-01 
• Deposition Author(s): Sillen, M., Weeks, S.D., Strelkov, S.V., Declerck, P.J.
• Funding Organization(s): Research Foundation - Flanders

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.03 Å
• R-Value Free: 0.250 
• R-Value Work: 0.208 
• R-Value Observed: 0.210 

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

• PubMed: 31858714 
• 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.

---

Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

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

Biological Assembly Evidence: SAXS

Macromolecule Content

• Total Structure Weight: 68.62 kDa 
• Atom Count: 4,676 
• Modelled Residue Count: 595 
• Deposited Residue Count: 616 
• Unique protein chains: 3

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-2g-42	B	116	Vicugna pacos	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
VHH-2w-64	C	121	Vicugna pacos	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.03 Å
• R-Value Free: 0.250 
• R-Value Work: 0.208 
• R-Value Observed: 0.210 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.483	α = 90
b = 71.424	β = 100.53
c = 96.598	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-01-01 
Deposition Author(s): Sillen, M., Weeks, S.D., Strelkov, S.V., Declerck, P.J.

---

Funding Organization	Location	Grant Number
Research Foundation - Flanders	Belgium	G072915N
Research Foundation - Flanders	Belgium	11ZQ916N

Revision History  

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