Structure of the tandem PH domains of Rtt106

Experimental Data Snapshot

  • Resolution: 1.43 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.182 

wwPDB Validation   3D Report Full Report

This is version 1.7 of the entry. See complete history


Structural basis for recognition of H3K56-acetylated histone H3-H4 by the chaperone Rtt106.

Su, D.Hu, Q.Li, Q.Thompson, J.R.Cui, G.Fazly, A.Davies, B.A.Botuyan, M.V.Zhang, Z.Mer, G.

(2012) Nature 483: 104-107

  • DOI: https://doi.org/10.1038/nature10861
  • Primary Citation of Related Structures:  
    2LH0, 3FSS, 3TVV, 3TW1

  • PubMed Abstract: 

    Dynamic variations in the structure of chromatin influence virtually all DNA-related processes in eukaryotes and are controlled in part by post-translational modifications of histones. One such modification, the acetylation of lysine 56 (H3K56ac) in the amino-terminal α-helix (αN) of histone H3, has been implicated in the regulation of nucleosome assembly during DNA replication and repair, and nucleosome disassembly during gene transcription. In Saccharomyces cerevisiae, the histone chaperone Rtt106 contributes to the deposition of newly synthesized H3K56ac-carrying H3-H4 complex on replicating DNA, but it is unclear how Rtt106 binds H3-H4 and specifically recognizes H3K56ac as there is no apparent acetylated lysine reader domain in Rtt106. Here, we show that two domains of Rtt106 are involved in a combinatorial recognition of H3-H4. An N-terminal domain homodimerizes and interacts with H3-H4 independently of acetylation while a double pleckstrin-homology (PH) domain binds the K56-containing region of H3. Affinity is markedly enhanced upon acetylation of K56, an effect that is probably due to increased conformational entropy of the αN helix of H3. Our data support a mode of interaction where the N-terminal homodimeric domain of Rtt106 intercalates between the two H3-H4 components of the (H3-H4)(2) tetramer while two double PH domains in the Rtt106 dimer interact with each of the two H3K56ac sites in (H3-H4)(2). We show that the Rtt106-(H3-H4)(2) interaction is important for gene silencing and the DNA damage response.

  • Organizational Affiliation

    Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota 55905, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Histone chaperone RTT106237Saccharomyces cerevisiaeMutation(s): 2 
Gene Names: N1346RTT106YNL206C
Find proteins for P40161 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P40161 
Go to UniProtKB:  P40161
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP40161
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.43 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.182 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.409α = 90
b = 92.206β = 105.16
c = 34.273γ = 90
Software Package:
Software NamePurpose
HKL-3000data collection
HKL-3000data reduction
HKL-3000data scaling

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-12-22
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.2: 2012-02-01
    Changes: Database references
  • Version 1.3: 2012-02-22
    Changes: Database references
  • Version 1.4: 2012-03-07
    Changes: Database references
  • Version 1.5: 2012-04-11
    Changes: Database references
  • Version 1.6: 2015-04-29
    Changes: Non-polymer description
  • Version 1.7: 2021-10-20
    Changes: Database references, Derived calculations