Crystal structure of Arabidopsis thaliana HDT3

Experimental Data Snapshot

  • Resolution: 1.80 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.191 

wwPDB Validation   3D Report Full Report

This is version 1.2 of the entry. See complete history


Plant-specific HDT family histone deacetylases are nucleoplasmins.

Bobde, R.C.Kumar, A.Vasudevan, D.

(2022) Plant Cell 34: 4760-4777

  • DOI: https://doi.org/10.1093/plcell/koac275
  • Primary Citation of Related Structures:  
    7VMF, 7VMH, 7VMI, 7VRR

  • PubMed Abstract: 

    Histone acetyltransferase (HAT)- and histone deacetylase (HDAC)-mediated histone acetylation and deacetylation regulate nucleosome dynamics and gene expression. HDACs are classified into different families, with HD-tuins or HDTs being specific to plants. HDTs show some sequence similarity to nucleoplasmins, the histone chaperones that aid in binding, storing, and loading H2A/H2B dimers to assemble nucleosomes. Here, we solved the crystal structure of the N-terminal domain (NTD) of all four HDTs (HDT1, HDT2, HDT3, and HDT4) from Arabidopsis (Arabidopsis thaliana). The NTDs form a nucleoplasmin fold, exist as pentamers in solution, and are resistant to protease treatment, high temperature, salt, and urea conditions. Structurally, HDTs do not form a decamer, unlike certain classical nucleoplasmins. The HDT-NTD requires an additional A2 acidic tract C-terminal to the nucleoplasmin domain for interaction with histone H3/H4 and H2A/H2B oligomers. We also report the in-solution structures of HDT2 pentamers in complex with histone oligomers. Our study provides a detailed structural and in vitro functional characterization of HDTs, revealing them to be nucleoplasmin family histone chaperones. The experimental confirmation that HDTs are nucleoplasmins may spark new interest in this enigmatic family of proteins.

  • Organizational Affiliation

    Institute of Life Sciences, Bhubaneswar, Odisha 751023, India.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Histone deacetylase HDT3
A, B, C, D, E
96Arabidopsis thalianaMutation(s): 0 
Gene Names: HDT3HD2CAt5g03740F17C15_160MED24.1
Find proteins for Q9LZR5 (Arabidopsis thaliana)
Explore Q9LZR5 
Go to UniProtKB:  Q9LZR5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9LZR5
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.80 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.191 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.623α = 90
b = 77.6β = 91.82
c = 55.511γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Department of Biotechnology (DBT, India)India--
Science and Engineering Research Board (SERB)India--

Revision History  (Full details and data files)

  • Version 1.0: 2022-09-21
    Type: Initial release
  • Version 1.1: 2022-12-14
    Changes: Database references
  • Version 1.2: 2023-11-29
    Changes: Data collection, Refinement description