9IH0 | pdb_00009ih0

Crystal structure of Vaspin with PolyP45


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.26 Å
  • R-Value Free: 
    0.240 (Depositor), 0.245 (DCC) 
  • R-Value Work: 
    0.218 (Depositor), 0.226 (DCC) 
  • R-Value Observed: 
    0.219 (Depositor) 

Starting Model: experimental
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Literature

Vaspin identified as a DNA-binding serpin with functional consequences for protease inhibition.

Mohlis, K.Useini, A.Betat, H.Bonin, S.Broghammer, H.Nuwayhid, R.Langer, S.Morl, M.Strater, N.Heiker, J.T.

(2025) FEBS J 

  • DOI: https://doi.org/10.1111/febs.70270
  • Primary Citation of Related Structures:  
    9IH0

  • PubMed Abstract: 

    Vaspin is highly expressed not only in the skin but also in the liver and adipose tissue. It counteracts inflammation and oxidative stress in inflammatory skin diseases, obesity, and associated metabolic disorders, in part by inhibiting the kallikrein proteases KLK7 and KLK14. Vaspin binds the cell-surface low-density lipoprotein receptor-related protein 1 (LRP1) with nanomolar affinity, and is rapidly internalized into adipocytes and other cells. We found intracellular vaspin partially localized in the nucleus. Since vaspin binds heparin and inorganic polyphosphates, we investigated the DNA binding of vaspin. Using DNA-affinity chromatography and differential radial capillary action of ligand assays, we found high-affinity binding to random sequences of single- and double-stranded DNA for both vaspin and KLK7. Furthermore, KLK7 inhibition was accelerated fivefold in the presence of DNA molecules at least 40 bases in length. We previously identified the heparin-binding site at a basic patch on the central beta-sheet A of vaspin. In the current work, we determined the crystal structure of polyphosphate P45-bound vaspin, which confirmed previously identified residues mutated to generate a nonheparin-binding (NHB) vaspin variant. While NHB vaspin failed to bind heparin and polyP45, it still bound DNA with high affinity and accelerated protease inhibition. Mutation of closely spaced basic residues in helix A and helix G did not significantly alter DNA binding. In conclusion, we have identified vaspin as the second human DNA-binding serpin. While the exact mode of the nonspecific interaction remains unclear, it accelerates protease inhibition and likely contributes to the nuclear localization observed for internalized vaspin and may allow for intracellular effects.


  • Organizational Affiliation
    • Helmholtz Institute for Metabolic, Obesity and Vascular Research (HI-MAG) of the Helmholtz Zentrum München at the University of Leipzig and University Hospital Leipzig, Germany.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Serpin A12
A, B
414Homo sapiensMutation(s): 0 
Gene Names: SERPINA12
UniProt & NIH Common Fund Data Resources
Find proteins for Q8IW75 (Homo sapiens)
Explore Q8IW75 
Go to UniProtKB:  Q8IW75
PHAROS:  Q8IW75
GTEx:  ENSG00000165953 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8IW75
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.26 Å
  • R-Value Free:  0.240 (Depositor), 0.245 (DCC) 
  • R-Value Work:  0.218 (Depositor), 0.226 (DCC) 
  • R-Value Observed: 0.219 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 143.257α = 90
b = 147.977β = 104.95
c = 62.464γ = 90
Software Package:
Software NamePurpose
STARANISOdata scaling
XDSdata reduction
PHASERphasing
REFMACrefinement
Cootmodel building
PHENIXrefinement

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)Germany209933838

Revision History  (Full details and data files)

  • Version 1.0: 2025-10-08
    Type: Initial release