The 97H/F mutant Structure of a glutamine-rich domain from histone deacetylase 4

Experimental Data Snapshot

  • Resolution: 3.00 Å
  • R-Value Free: 0.327 
  • R-Value Work: 0.305 
  • R-Value Observed: 0.324 

Starting Model: experimental
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Crystal structure of a conserved N-terminal domain of histone deacetylase 4 reveals functional insights into glutamine-rich domains.

Guo, L.Han, A.Bates, D.L.Cao, J.Chen, L.

(2007) Proc Natl Acad Sci U S A 104: 4297-4302

  • DOI: https://doi.org/10.1073/pnas.0608041104
  • Primary Citation of Related Structures:  
    2H8N, 2O94

  • PubMed Abstract: 

    Glutamine-rich sequences exist in a wide range of proteins across multiple species. A subset of glutamine-rich sequences has been shown to form amyloid fibers implicated in human diseases. The physiological functions of these sequence motifs are not well understood, partly because of the lack of structural information. Here we have determined a high-resolution structure of a glutamine-rich domain from human histone deacetylase 4 (HDAC4) by x-ray crystallography. The glutamine-rich domain of HDAC4 (19 glutamines of 68 residues) folds into a straight alpha-helix that assembles as a tetramer. In contrast to most coiled coil proteins, the HDAC4 tetramer lacks regularly arranged apolar residues and an extended hydrophobic core. Instead, the protein interfaces consist of multiple hydrophobic patches interspersed with polar interaction networks, wherein clusters of glutamines engage in extensive intra- and interhelical interactions. In solution, the HDAC4 tetramer undergoes rapid equilibrium with monomer and intermediate species. Structure-guided mutations that expand or disrupt hydrophobic patches drive the equilibrium toward the tetramer or monomer, respectively. We propose that a general role of glutamine-rich motifs be to mediate protein-protein interactions characteristic of a large component of polar interaction networks that may facilitate reversible assembly and disassembly of protein complexes.

  • Organizational Affiliation

    Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309-0215, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Histone deacetylase 4
A, B, C, D
112Homo sapiensMutation(s): 1 
Gene Names: HDAC4KIAA0288
UniProt & NIH Common Fund Data Resources
Find proteins for P56524 (Homo sapiens)
Explore P56524 
Go to UniProtKB:  P56524
GTEx:  ENSG00000068024 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP56524
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 3.00 Å
  • R-Value Free: 0.327 
  • R-Value Work: 0.305 
  • R-Value Observed: 0.324 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 189.885α = 90
b = 61.023β = 108.61
c = 60.777γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
ADSCdata collection
HKL-2000data reduction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-02-27
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-18
    Changes: Refinement description
  • Version 1.4: 2021-10-20
    Changes: Database references
  • Version 1.5: 2023-08-30
    Changes: Data collection, Refinement description