2IDC | pdb_00002idc

Structure of the Histone H3-Asf1 Chaperone Interaction


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 
    0.239 (Depositor), 0.243 (DCC) 
  • R-Value Work: 
    0.194 (Depositor), 0.197 (DCC) 
  • R-Value Observed: 
    0.196 (Depositor) 

Starting Model: experimental
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This is version 1.4 of the entry. See complete history

Literature

Structure of the yeast histone H3-ASF1 interaction: implications for chaperone mechanism, species-specific interactions, and epigenetics.

Antczak, A.J.Tsubota, T.Kaufman, P.D.Berger, J.M.

(2006) BMC Struct Biol 6: 26-26

  • DOI: https://doi.org/10.1186/1472-6807-6-26
  • Primary Citation Related Structures: 
    2IDC

  • PubMed Abstract: 

    The histone H3/H4 chaperone Asf1 (anti-silencing function 1) is required for the establishment and maintenance of proper chromatin structure, as well as for genome stability in eukaryotes. Asf1 participates in both DNA replication-coupled (RC) and replication-independent (RI) histone deposition reactions in vitro and interacts with complexes responsible for both pathways in vivo. Asf1 is known to directly bind histone H3, however, high-resolution structural information about the geometry of this interaction was previously unknown. Here we report the structure of a histone/histone chaperone interaction. We have solved the 2.2 A crystal structure of the conserved N-terminal immunoglobulin fold domain of yeast Asf1 (residues 2-155) bound to the C-terminal helix of yeast histone H3 (residues 121-134). The structure defines a histone-binding patch on Asf1 consisting of both conserved and yeast-specific residues; mutation of these residues abrogates H3/H4 binding affinity. The geometry of the interaction indicates that Asf1 binds to histones H3/H4 in a manner that likely blocks sterically the H3/H3 interface of the nucleosomal four-helix bundle. These data clarify how Asf1 regulates histone stoichiometry to modulate epigenetic inheritance. The structure further suggests a physical model in which Asf1 contributes to interpretation of a "histone H3 barcode" for sorting H3 isoforms into different deposition pathways.


  • Organizational Affiliation
    • Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, USA. antczaka@berkeley.edu <antczaka@berkeley.edu>

Macromolecule Content 

  • Total Structure Weight: 20.08 kDa 
  • Atom Count: 1,429 
  • Modeled Residue Count: 167 
  • Deposited Residue Count: 179 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
ANTI-SILENCING PROTEIN 1 AND HISTONE H3 CHIMERA179Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: 
UniProt
Find proteins for P32447 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P32447 
Go to UniProtKB:  P32447
Find proteins for P61830 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P61830 
Go to UniProtKB:  P61830
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP61830P32447
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free:  0.239 (Depositor), 0.243 (DCC) 
  • R-Value Work:  0.194 (Depositor), 0.197 (DCC) 
  • R-Value Observed: 0.196 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.431α = 90
b = 52.094β = 90
c = 86.676γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
Blu-Icedata collection
MOSFLMdata reduction
CCP4data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-01-30
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.3: 2017-06-14
    Changes: Database references, Source and taxonomy, Structure summary
  • Version 1.4: 2023-08-30
    Changes: Data collection, Database references, Refinement description