Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content

• Total Structure Weight: 88.58 kDa 
• Atom Count: 3254 
• Modelled Residue Count: 360 
• Deposited Residue Count: 794 
• Unique protein chains: 1

5G0H

Crystal structure of Danio rerio HDAC6 CD2 in complex with (S)- trichostatin A

• PDB DOI: 10.2210/pdb5G0H/pdb

• Classification: CELL CYCLE
• Organism(s): Danio rerio
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2016-03-18 Released: 2016-07-27 
• Deposition Author(s): Miyake, Y., Keusch, J.J., Wang, L., Saito, M., Hess, D., Wang, X., Melancon, B.J., Helquist, P., Gut, H., Matthias, P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.174 
• R-Value Work: 0.150 
• R-Value Observed: 0.151 

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

• PubMed: 27454931 
• DOI: 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.

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Organizational Affiliation: 

Faculty of Sciences, University of Basel, Basel, Switzerland.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HDAC6	A	794	Danio rerio	Mutation(s): 0  Gene Names: hdac6
UniProt
Find proteins for F8W4B7 (Danio rerio) Explore F8W4B7  Go to UniProtKB:  F8W4B7

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
E1Z	B [auth A]	S-Trichostatin A C17 H22 N2 O3 RTKIYFITIVXBLE-LEJRBOCMSA-N
ZN	E [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO	F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
K	C [auth A], D [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
E1Z	Binding MOAD:  5G0H	IC50: 9.88 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.174 
• R-Value Work: 0.150 
• R-Value Observed: 0.151 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.98	α = 90
b = 48.23	β = 103.22
c = 73.78	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2016-03-18 
• Released Date: 2016-07-27 
Deposition Author(s): Miyake, Y., Keusch, J.J., Wang, L., Saito, M., Hess, D., Wang, X., Melancon, B.J., Helquist, P., Gut, H., Matthias, P.

Revision History  

• 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