7ZYU

HDAC6 ZnF domain inhibitor - DARPin (Designed Ankyrin repeat protein) F10


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.43 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.218 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Disrupting the HDAC6-ubiquitin interaction impairs infection by influenza and Zika virus and cellular stress pathways.

Wang, L.Moreira, E.A.Kempf, G.Miyake, Y.Oliveira Esteves, B.I.Fahmi, A.Schaefer, J.V.Dreier, B.Yamauchi, Y.Alves, M.P.Pluckthun, A.Matthias, P.

(2022) Cell Rep 39: 110736-110736

  • DOI: https://doi.org/10.1016/j.celrep.2022.110736
  • Primary Citation of Related Structures:  
    7ZYU

  • PubMed Abstract: 

    The deacetylase HDAC6 has tandem catalytic domains and a zinc finger domain (ZnF) binding ubiquitin (Ub). While the catalytic domain has an antiviral effect, the ZnF facilitates influenza A virus (IAV) infection and cellular stress responses. By recruiting Ub via the ZnF, HDAC6 promotes the formation of aggresomes and stress granules (SGs), dynamic structures associated with pathologies such as neurodegeneration. IAV subverts the aggresome/HDAC6 pathway to facilitate capsid uncoating during early infection. To target this pathway, we generate designed ankyrin repeat proteins (DARPins) binding the ZnF; one of these prevents interaction with Ub in vitro and in cells. Crystallographic analysis shows that it blocks the ZnF pocket where Ub engages. Conditional expression of this DARPin reversibly impairs infection by IAV and Zika virus; moreover, SGs and aggresomes are downregulated. These results validate the HDAC6 ZnF as an attractive target for drug discovery.


  • Organizational Affiliation

    Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland; Faculty of Sciences, University of Basel, 4031 Basel, Switzerland.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Histone deacetylase 6110Homo sapiensMutation(s): 0 
Gene Names: HDAC6KIAA0901JM21
EC: 3.5.1.98 (PDB Primary Data), 3.5.1 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UBN7 (Homo sapiens)
Explore Q9UBN7 
Go to UniProtKB:  Q9UBN7
PHAROS:  Q9UBN7
GTEx:  ENSG00000094631 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UBN7
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Designed Ankyrin repeat protein F10162synthetic constructMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.43 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.218 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.391α = 90
b = 81.391β = 90
c = 103.644γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
autoPROCdata reduction
STARANISOdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swiss National Science FoundationSwitzerland2014/264

Revision History  (Full details and data files)

  • Version 1.0: 2022-06-01
    Type: Initial release
  • Version 1.1: 2024-01-31
    Changes: Data collection, Refinement description
  • Version 1.2: 2024-03-27
    Changes: Database references
  • Version 1.3: 2024-10-09
    Changes: Structure summary