7XAY | pdb_00007xay

Crystal structure of Hat1-Hat2-Asf1-H3-H4

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 
    0.256 (Depositor), 0.260 (DCC) 
  • R-Value Work: 
    0.230 (Depositor), 0.230 (DCC) 
  • R-Value Observed: 
    0.232 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 

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Literature

Topography of histone H3-H4 interaction with the Hat1-Hat2 acetyltransferase complex.

Yue, Y., Yang, W.S., Zhang, L., Liu, C.P., Xu, R.M.

(2022) Genes Dev 36: 408-413

  • DOI: https://doi.org/10.1101/gad.349099.121
  • Primary Citation of Related Structures:  
    7XAY

  • PubMed Abstract: 

    Chaperones influence histone conformation and intermolecular interaction in multiprotein complexes, and the structures obtained with full-length histones often provide more accurate and comprehensive views. Here, our structure of the Hat1-Hat2 acetyltransferase complex bound to Asf1-H3-H4 shows that the core domains of H3 and H4 are involved in binding Hat1 and Hat2, and the N-terminal tail of H3 makes extensive interaction with Hat2. These findings expand the knowledge about histone-protein interaction and implicate a function of Hat2/RbAp46/48, which is a versatile histone chaperone found in many chromatin-associated complexes, in the passing of histones between chaperones.

    • Organizational Affiliation: 

    National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Soluble cytochrome b562,Histone acetyltransferase type B catalytic subunit416Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: cybC, HAT1, YPL001W, LPA16W, YP8132.12
EC: 2.3.1.48
UniProt
Find proteins for P0ABE7 (Escherichia coli)
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Find proteins for Q12341 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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UniProt GroupsQ12341P0ABE7
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Histone acetyltransferase type B subunit 2401Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: HAT2, YEL056W
UniProt
Find proteins for P39984 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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UniProt GroupP39984
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Histone chaperone asf1154Aspergillus fumigatus Af293Mutation(s): 0 
Gene Names: asf1, AFUA_3G11030
UniProt
Find proteins for Q4WXX5 (Aspergillus fumigatus (strain ATCC MYA-4609 / CBS 101355 / FGSC A1100 / Af293))
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H3135Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: HHT1, YBR010W, YBR0201, HHT2, SIN2, YNL031C, N2749
UniProt
Find proteins for P61830 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H496Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: HHF1, YBR009C, YBR0122, HHF2, YNL030W, N2752
UniProt
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UniProt GroupP02309
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Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
COA (Subject of Investigation/LOI)
Query on COA
Download Ideal Coordinates CCD File 
F [auth A]COENZYME A
C21 H36 N7 O16 P3 S
RGJOEKWQDUBAIZ-IBOSZNHHSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free:  0.256 (Depositor), 0.260 (DCC) 
  • R-Value Work:  0.230 (Depositor), 0.230 (DCC) 
  • R-Value Observed: 0.232 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 96.41α = 90
b = 124.684β = 90
c = 161.066γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted COAClick on this verticalbar to view details

View more in-depth experimental data
Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China91853204

Revision History  (Full details and data files)

  • Version 1.0: 2022-05-18
    Type: Initial release
  • Version 1.1: 2023-11-29
    Changes: Data collection, Refinement description