2YGV | pdb_00002ygv

Conserved N-terminal domain of the yeast Histone Chaperone Asf1 in complex with the C-terminal fragment of Rad53


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.94 Å
  • R-Value Free: 
    0.257 (Depositor), 0.273 (DCC) 
  • R-Value Work: 
    0.188 (Depositor), 0.199 (DCC) 
  • R-Value Observed: 
    0.191 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history

Literature

Surprising Complexity of the Asf1 Histone Chaperone-Rad53 Kinase Interaction

Jiao, Y.Seeger, K.Lautrette, A.Gaubert, A.Mousson, F.Guerois, R.Mann, C.Ochsenbein, F.

(2012) Proc Natl Acad Sci U S A 109: 2866

  • DOI: https://doi.org/10.1073/pnas.1106023109
  • Primary Citation Related Structures: 
    2YGV

  • PubMed Abstract: 

    The histone chaperone Asf1 and the checkpoint kinase Rad53 are found in a complex in budding yeast cells in the absence of genotoxic stress. Our data suggest that this complex involves at least three interaction sites. One site involves the H3-binding surface of Asf11 with an as yet undefined surface of Rad53. A second site is formed by the Rad53-FHA1 domain binding to Asf1-T(270) phosphorylated by casein kinase II. The third site involves the C-terminal 21 amino acids of Rad53 bound to the conserved Asf1 N-terminal domain. The structure of this site showed that the Rad53 C-terminus binds Asf1 in a remarkably similar manner to peptides derived from the histone cochaperones HirA and CAF-I. We call this binding motif, (R/K)R(I/A/V) (L/P), the AIP box for Asf1-Interacting Protein box. Furthermore, C-terminal Rad53-F(820) binds the same pocket of Asf1 as does histone H4-F(100). Thus Rad53 competes with histones H3-H4 and cochaperones HirA/CAF-I for binding to Asf1. Rad53 is phosphorylated and activated upon genotoxic stress. The Asf1-Rad53 complex dissociated when cells were treated with hydroxyurea but not methyl-methane-sulfonate, suggesting a regulation of the complex as a function of the stress. We identified a rad53 mutation that destabilized the Asf1-Rad53 complex and increased the viability of rad9 and rad24 mutants in conditions of genotoxic stress, suggesting that complex stability impacts the DNA damage response.


  • Organizational Affiliation
    • Commissariat à l'Energie Atomique, iBiTec-S, Service de Biologie Intégrative et de Génétique Moléculaire, Gif-sur-Yvette F-91191, France.

Macromolecule Content 

  • Total Structure Weight: 81.96 kDa 
  • Atom Count: 5,400 
  • Modeled Residue Count: 672 
  • Deposited Residue Count: 720 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
HISTONE CHAPERONE ASF1
A, B, C, D
158Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P32447 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P32447 
Go to UniProtKB:  P32447
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP32447
Sequence Annotations
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Reference Sequence
Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
SERINE/THREONINE-PROTEIN KINASE RAD53
E, F, G, H
22Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7.11.1 (PDB Primary Data), 2.7.12.1 (UniProt)
UniProt
Find proteins for P22216 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P22216 
Go to UniProtKB:  P22216
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP22216
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.94 Å
  • R-Value Free:  0.257 (Depositor), 0.273 (DCC) 
  • R-Value Work:  0.188 (Depositor), 0.199 (DCC) 
  • R-Value Observed: 0.191 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 125.24α = 90
b = 98.18β = 132.49
c = 86.49γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
XDSdata scaling
MOLREPphasing

Structure Validation

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Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2012-02-15
    Type: Initial release
  • Version 1.1: 2012-03-07
    Changes: Other
  • Version 1.2: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description