Crystal structure of the S. cerevisiae Rtf1 histone modification domain mutant R126A

Experimental Data Snapshot

  • Resolution: 1.62 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.147 
  • R-Value Observed: 0.149 

Starting Model: experimental
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The Histone Modification Domain of Paf1 Complex Subunit Rtf1 Directly Stimulates H2B Ubiquitylation through an Interaction with Rad6.

Van Oss, S.B.Shirra, M.K.Bataille, A.R.Wier, A.D.Yen, K.Vinayachandran, V.Byeon, I.L.Cucinotta, C.E.Heroux, A.Jeon, J.Kim, J.VanDemark, A.P.Pugh, B.F.Arndt, K.M.

(2016) Mol Cell 64: 815-825

  • DOI: https://doi.org/10.1016/j.molcel.2016.10.008
  • Primary Citation of Related Structures:  
    5E8B, 5EMX

  • PubMed Abstract: 

    The five-subunit yeast Paf1 complex (Paf1C) regulates all stages of transcription and is critical for the monoubiquitylation of histone H2B (H2Bub), a modification that broadly influences chromatin structure and eukaryotic transcription. Here, we show that the histone modification domain (HMD) of Paf1C subunit Rtf1 directly interacts with the ubiquitin conjugase Rad6 and stimulates H2Bub independently of transcription. We present the crystal structure of the Rtf1 HMD and use site-specific, in vivo crosslinking to identify a conserved Rad6 interaction surface. Utilizing ChIP-exo analysis, we define the localization patterns of the H2Bub machinery at high resolution and demonstrate the importance of Paf1C in targeting the Rtf1 HMD, and thereby H2Bub, to its appropriate genomic locations. Finally, we observe HMD-dependent stimulation of H2Bub in a transcription-free, reconstituted in vitro system. Taken together, our results argue for an active role for Paf1C in promoting H2Bub and ensuring its proper localization in vivo.

  • Organizational Affiliation

    Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
RNA polymerase-associated protein RTF1
A, B
67Saccharomyces cerevisiae S288CMutation(s): 1 
Gene Names: RTF1CSL3YGL244WHRA458
Find proteins for P53064 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P53064 
Go to UniProtKB:  P53064
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP53064
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.62 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.147 
  • R-Value Observed: 0.149 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 93.868α = 90
b = 93.868β = 90
c = 75.344γ = 120
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-11-09
    Type: Initial release
  • Version 1.1: 2017-01-25
    Changes: Database references
  • Version 1.2: 2023-09-27
    Changes: Data collection, Database references, Derived calculations, Refinement description