7QNO

Crystal structure of ligand-free Danio rerio HDAC6 CD1 CD2

• PDB DOI: https://doi.org/10.2210/pdb7QNO/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Danio rerio
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2021-12-21 Released: 2022-02-09 
• Deposition Author(s): Kempf, G., Langousis, G., Sanchez, J., Matthias, P.
• Funding Organization(s): Other private

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.38 Å
• R-Value Free: 0.228 
• R-Value Work: 0.212 
• R-Value Observed: 0.213 

Literature

Expression and Crystallization of HDAC6 Tandem Catalytic Domains.

Langousis, G., Sanchez, J., Kempf, G., Matthias, P.

(2023) Methods Mol Biol 2589: 467-480

• PubMed: 36255643 
• DOI: https://doi.org/10.1007/978-1-0716-2788-4_30
• Primary Citation of Related Structures:  
  7QNO


• PubMed Abstract: 
  

  Histone deacetylase 6 (HDAC6) is an atypical lysine deacetylase with tandem catalytic domains and an ubiquitin-binding zinc finger domain. HDAC6 is involved in various biological processes, such as cell motility or stress responses, and has been implicated in pathologies ranging from cancer to neurodegeneration. Due to this broad range of functions, there has been considerable interest in developing HDAC6-specific small molecule inhibitors, several of which are already available. The crystal structure of the tandem catalytic domains of zebrafish HDAC6 has revealed an arrangement with twofold symmetry and extensive surface interaction between the catalytic domains. Further dissection of the biochemical properties of HDAC6 and the development of novel inhibitors will benefit from being able to routinely express high-quality protein. We present here our optimized protocol for expression and crystallization of the zebrafish tandem catalytic domains.

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Organizational Affiliation: 

Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 92.84 kDa 
• Atom Count: 5,953 
• Modelled Residue Count: 755 
• Deposited Residue Count: 837 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone deacetylase 6	A	837	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
PRO	B [auth A]	PROLINE C5 H9 N O2 ONIBWKKTOPOVIA-BYPYZUCNSA-N
GOL	H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN	E [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
K	C [auth A], D [auth A], F [auth A], G [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.38 Å
• R-Value Free: 0.228 
• R-Value Work: 0.212 
• R-Value Observed: 0.213 
• Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 186.134	α = 90
b = 186.134	β = 90
c = 102.442	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
Coot	model building
autoPROC	data reduction
STARANISO	data scaling
PHASER	phasing
ISOLDE	refinement
XDS	data reduction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-02-09 
Deposition Author(s): Kempf, G., Langousis, G., Sanchez, J., Matthias, P.

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Funding Organization	Location	Grant Number
Other private		--

Revision History  

• Version 1.0: 2022-02-09
  Type: Initial release
  
• Version 1.1: 2022-11-23
  Changes: Database references, Refinement description
• Version 1.2: 2024-01-31
  Changes: Data collection, Refinement description