In-solution structure and oligomerization of human histone deacetylase 6 - an integrative approach.

Shukla S, Komarek J, Novakova Z, Nedvedova J, Ustinova K, Vankova P, Kadek A, Uetrecht C, Mertens H, Barinka C, FEBS J (2022) Europe PMC

SASDMX7 – Human histone deacetylase 6

Histone deacetylase 6
MWexperimental 163 kDa
MWexpected 131 kDa
VPorod 316 nm3
log I(s) 2.08×10-2 2.08×10-3 2.08×10-4 2.08×10-5
Histone deacetylase 6 small angle scattering data  s, nm-1
ln I(s)
Histone deacetylase 6 Guinier plot ln 2.08×10-2 Rg: 7.0 nm 0 (7.0 nm)-2 s2
(sRg)2I(s)/I(0)
Histone deacetylase 6 Kratky plot 1.104 0 √3 sRg
p(r)
Histone deacetylase 6 pair distance distribution function Rg: 7.5 nm 0 Dmax: 26 nm

Data validation

Fits and models

log I(s)
 s, nm-1
Human histone deacetylase 6 Rg histogram Rg, nm
Histone deacetylase 6 EOM/RANCH model
Histone deacetylase 6 EOM/RANCH model
Histone deacetylase 6 EOM/RANCH model
Histone deacetylase 6 EOM/RANCH model
Histone deacetylase 6 EOM/RANCH model
Histone deacetylase 6 EOM/RANCH model
Synchrotron SAXS data from solutions of histone deacetylase 6 in 30 mM HEPES, 140 mM NaCl, 10 mM KCl, 0.25 mM TCEP, pH 7.4 were collected on the EMBL P12 beam line at PETRA III (Hamburg, Germany) using a Pilatus 6M detector at a sample-detector distance of 3 m and at a wavelength of λ = 0.124 nm (I(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). In-line size-exclusion chromatography (SEC) SAS was employed. The SEC parameters were as follows: A 95.00 μl sample at 4.6 mg/ml was injected at a 0.60 ml/min flow rate onto a GE Superose 6 Increase 10/300 column at 20°C. 2400 successive 1 second frames were collected. The data were normalized to the intensity of the transmitted beam and radially averaged; the scattering of the solvent-blank was subtracted.

Histone deacetylase 6 (HDAC6)
Mol. type   Protein
Organism   Homo sapiens
Olig. state   Monomer
Mon. MW   131.3 kDa
 
UniProt   Q9UBN7 (2-1215)
Sequence   FASTA