5G0F

Crystal structure of Danio rerio HDAC6 ZnF-UBP domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.180 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Structural Insights Into Hdac6 Tubulin Deacetylation and its Selective Inhibition

Miyake, Y.Keusch, J.J.Wang, L.Saito, M.Hess, D.Wang, X.Melancon, B.J.Helquist, P.Gut, H.Matthias, P.

(2016) Nat Chem Biol 12: 748

  • DOI: https://doi.org/10.1038/nchembio.2140
  • Primary Citation of Related Structures:  
    5G0F, 5G0G, 5G0H, 5G0I, 5G0J

  • PubMed Abstract: 

    We report crystal structures of zebrafish histone deacetylase 6 (HDAC6) catalytic domains in tandem or as single domains in complex with the (R) and (S) enantiomers of trichostatin A (TSA) or with the HDAC6-specific inhibitor nexturastat A. The tandem domains formed, together with the inter-domain linker, an ellipsoid-shaped complex with pseudo-twofold symmetry. We identified important active site differences between both catalytic domains and revealed the binding mode of HDAC6 selective inhibitors. HDAC inhibition assays with (R)- and (S)-TSA showed that (R)-TSA was a broad-range inhibitor, whereas (S)-TSA had moderate selectivity for HDAC6. We identified a uniquely positioned α-helix and a flexible tryptophan residue in the loop joining α-helices H20 to H21 as critical for deacetylation of the physiologic substrate tubulin. Using single-molecule measurements and biochemical assays we demonstrated that HDAC6 catalytic domain 2 deacetylated α-tubulin lysine 40 in the lumen of microtubules, but that its preferred substrate was unpolymerized tubulin.


  • Organizational Affiliation

    Friedrich Miescher Institute for Biomedical Research (FMI), Basel, Switzerland.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
HDAC6110Danio rerioMutation(s): 0 
UniProt
Find proteins for F8W4B7 (Danio rerio)
Explore F8W4B7 
Go to UniProtKB:  F8W4B7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupF8W4B7
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.180 
  • Space Group: I 2 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 100.74α = 90
b = 100.74β = 90
c = 100.74γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-07-27
    Type: Initial release
  • Version 1.1: 2016-08-10
    Changes: Database references
  • Version 1.2: 2016-09-28
    Changes: Database references
  • Version 1.3: 2019-01-23
    Changes: Advisory, Data collection, Derived calculations, Other
  • Version 1.4: 2024-01-10
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description