3Q33

Structure of the Rtt109-AcCoA/Vps75 Complex and Implications for Chaperone-Mediated Histone Acetylation


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.195 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structure of the Rtt109-AcCoA/Vps75 Complex and Implications for Chaperone-Mediated Histone Acetylation.

Tang, Y.Holbert, M.A.Delgoshaie, N.Wurtele, H.Guillemette, B.Meeth, K.Yuan, H.Drogaris, P.Lee, E.H.Durette, C.Thibault, P.Verreault, A.Cole, P.A.Marmorstein, R.

(2011) Structure 19: 221-231

  • DOI: https://doi.org/10.1016/j.str.2010.12.012
  • Primary Citation of Related Structures:  
    3Q33, 3Q35

  • PubMed Abstract: 

    Yeast Rtt109 promotes nucleosome assembly and genome stability by acetylating K9, K27, and K56 of histone H3 through interaction with either of two distinct histone chaperones, Vps75 or Asf1. We report the crystal structure of an Rtt109-AcCoA/Vps75 complex revealing an elongated Vps75 homodimer bound to two globular Rtt109 molecules to form a symmetrical holoenzyme with a ∼12 Å diameter central hole. Vps75 and Rtt109 residues that mediate complex formation in the crystals are also important for Rtt109-Vps75 interaction and H3K9/K27 acetylation both in vitro and in yeast cells. The same Rtt109 residues do not participate in Asf1-mediated Rtt109 acetylation in vitro or H3K56 acetylation in yeast cells, demonstrating that Asf1 and Vps75 dictate Rtt109 substrate specificity through distinct mechanisms. These studies also suggest that Vps75 binding stimulates Rtt109 catalytic activity by appropriately presenting the H3-H4 substrate within the central cavity of the holoenzyme to promote H3K9/K27 acetylation of new histones before deposition.


  • Organizational Affiliation

    Program in Gene Expression and Regulation, The Wistar Institute, Philadelphia, PA 19104, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Histone acetyltransferase RTT109438Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: KIM2L1377REM50RTT109SCY_3578YLL002W
EC: 2.3.1.48
UniProt
Find proteins for Q07794 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q07794 
Go to UniProtKB:  Q07794
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ07794
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Vacuolar protein sorting-associated protein 75232Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: N0890VPS75YNL246W
UniProt
Find proteins for P53853 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P53853 
Go to UniProtKB:  P53853
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP53853
Sequence Annotations
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  • Reference Sequence

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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
HISTONE H3C [auth D]15synthetic constructMutation(s): 0 
UniProt
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 GroupP61830
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ACO
Query on ACO

Download Ideal Coordinates CCD File 
D [auth A]ACETYL COENZYME *A
C23 H38 N7 O17 P3 S
ZSLZBFCDCINBPY-ZSJPKINUSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
E [auth A]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
ALY
Query on ALY
A
L-PEPTIDE LINKINGC8 H16 N2 O3LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.195 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 97.543α = 90
b = 119.57β = 90
c = 80.566γ = 90
Software Package:
Software NamePurpose
Blu-Icedata collection
AMoREphasing
PHENIXrefinement
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-02-02
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.3: 2023-12-06
    Changes: Data collection