6THL

Crystal structure of the complex between RTT106 and BCD1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.300 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.219 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

The box C/D snoRNP assembly factor Bcd1 interacts with the histone chaperone Rtt106 and controls its transcription dependent activity.

Bragantini, B.Charron, C.Bourguet, M.Paul, A.Tiotiu, D.Rothe, B.Marty, H.Terral, G.Hessmann, S.Decourty, L.Chagot, M.E.Strub, J.M.Massenet, S.Bertrand, E.Quinternet, M.Saveanu, C.Cianferani, S.Labialle, S.Manival, X.Charpentier, B.

(2021) Nat Commun 12: 1859-1859

  • DOI: https://doi.org/10.1038/s41467-021-22077-4
  • Primary Citation of Related Structures:  
    6NZ2, 6THL

  • PubMed Abstract: 

    Biogenesis of eukaryotic box C/D small nucleolar ribonucleoproteins initiates co-transcriptionally and requires the action of the assembly machinery including the Hsp90/R2TP complex, the Rsa1p:Hit1p heterodimer and the Bcd1 protein. We present genetic interactions between the Rsa1p-encoding gene and genes involved in chromatin organization including RTT106 that codes for the H3-H4 histone chaperone Rtt106p controlling H3K56ac deposition. We show that Bcd1p binds Rtt106p and controls its transcription-dependent recruitment by reducing its association with RNA polymerase II, modulating H3K56ac levels at gene body. We reveal the 3D structures of the free and Rtt106p-bound forms of Bcd1p using nuclear magnetic resonance and X-ray crystallography. The interaction is also studied by a combination of biophysical and proteomic techniques. Bcd1p interacts with a region that is distinct from the interaction interface between the histone chaperone and histone H3. Our results are evidence for a protein interaction interface for Rtt106p that controls its transcription-associated activity.


  • Organizational Affiliation

    Université de Lorraine, CNRS, IMoPA, Nancy, France.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Rtt106p240Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: RTT106C1Q_03707
UniProt
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
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Box C/D snoRNA protein 1185Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: BCD1YHR040W
UniProt
Find proteins for P38772 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P38772 
Go to UniProtKB:  P38772
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP38772
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.300 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.219 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.712α = 90
b = 66.684β = 104.72
c = 65.122γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XPREPdata scaling
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-12-02
    Type: Initial release
  • Version 1.1: 2021-06-16
    Changes: Database references
  • Version 1.2: 2024-01-24
    Changes: Data collection, Database references, Refinement description