Biological Assembly 1  

 3D View: Structure | Electron Density

Global Symmetry: Dihedral - D2  (3D View)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content

• Total Structure Weight: 54.65 kDa 
• Atom Count: 2328 
• Modelled Residue Count: 272 
• Deposited Residue Count: 448 
• Unique protein chains: 1

2O94

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

• DOI: 10.2210/pdb2O94/pdb

• Classification: TRANSCRIPTION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2006-12-13 Released: 2007-02-27 
• Deposition Author(s): Guo, L., Han, A., Bates, D.L., Chen, L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 0.327 
• R-Value Work: 0.305 
• R-Value Observed: 0.324 

Literature

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

• PubMed: 17360518 
• DOI: 10.1073/pnas.0608041104
• Primary Citation of Related Structures:  
  2O94, 2H8N


• 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone deacetylase 4	A, B, C, D	112	Homo sapiens	Mutation(s): 1  Gene Names: HDAC4, KIAA0288 EC: 3.5.1.98
Find proteins for P56524 (Homo sapiens) Explore P56524  Go to UniProtKB:  P56524
NIH Common Fund Data Resources
PHAROS:  P56524 GTEx:  ENSG00000068024

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• 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 = 189.885	α = 90
b = 61.023	β = 108.61
c = 60.777	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
HKL-2000	data reduction
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2006-12-13 
• Released Date: 2007-02-27 
Deposition Author(s): Guo, L., Han, A., Bates, D.L., Chen, L.

Revision History  

• 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