4PSX

Crystal structure of histone acetyltransferase complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.51 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.183 

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Literature

Hat2p recognizes the histone H3 tail to specify the acetylation of the newly synthesized H3/H4 heterodimer by the Hat1p/Hat2p complex

Li, Y.Zhang, L.Liu, T.Chai, C.Fang, Q.Wu, H.Agudelo garcia, P.A.Han, Z.Zong, S.Yu, Y.Zhang, X.Parthun, M.R.Chai, J.Xu, R.M.Yang, M.

(2014) Genes Dev 28: 1217-1227

  • DOI: https://doi.org/10.1101/gad.240531.114
  • Primary Citation of Related Structures:  
    4PSW, 4PSX

  • PubMed Abstract: 

    Post-translational modifications of histones are significant regulators of replication, transcription, and DNA repair. Particularly, newly synthesized histone H4 in H3/H4 heterodimers becomes acetylated on N-terminal lysine residues prior to its incorporation into chromatin. Previous studies have established that the histone acetyltransferase (HAT) complex Hat1p/Hat2p medicates this modification. However, the mechanism of how Hat1p/Hat2p recognizes and facilitates the enzymatic activities on the newly assembled H3/H4 heterodimer remains unknown. Furthermore, Hat2p is a WD40 repeat protein, which is found in many histone modifier complexes. However, how the WD40 repeat proteins facilitate enzymatic activities of histone modification enzymes is unclear. In this study, we first solved the high-resolution crystal structure of a Hat1p/Hat2p/CoA/H4 peptide complex and found that the H4 tail interacts with both Hat1p and Hat2p, by which substrate recruitment is facilitated. We further discovered that H3 N-terminal peptides can bind to the Hat2p WD40 domain and solved the structure of the Hat1p/Hat2p/CoA/H4/H3 peptide complex. Moreover, the interaction with Hat2p requires unmodified Arg2/Lys4 and Lys9 on the H3 tail, suggesting a novel model to specify the activity of Hat1p/Hat2p toward newly synthesized H3/H4 heterodimers. Together, our study demonstrated the substrate recognition mechanism by the Hat1p/Hat2p complex, which is critical for DNA replication and other chromatin remodeling processes.


  • Organizational Affiliation

    Ministry of Education Key Laboratory of Protein Sciences, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China;


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Histone acetyltransferase type B catalytic subunit
A, D
320Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: HAT1LPA16WYP8132.12YPL001W
EC: 2.3.1.48
UniProt
Find proteins for Q12341 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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UniProt GroupQ12341
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Histone acetyltransferase type B subunit 2
B, E
401Saccharomyces cerevisiae S288CMutation(s): 1 
Gene Names: HAT2YEL056W
UniProt
Find proteins for P39984 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H4
C, F
48Saccharomyces cerevisiae S288CMutation(s): 1 
Gene Names: HHF1YBR009CYBR0122HHF2YNL030WN2752
UniProt
Find proteins for P02309 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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  • Reference Sequence

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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H3G [auth Y],
H [auth P]
15Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P61830 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P61830 
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UniProt GroupP61830
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.51 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.183 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.548α = 75.97
b = 85.331β = 72.4
c = 114.51γ = 66.06
Software Package:
Software NamePurpose
Blu-Icedata collection
PHASESphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-07-09
    Type: Initial release
  • Version 1.1: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description