3Q35 | pdb_00003q35

Structure of the Rtt109-AcCoA/Vps75 complex and implications for chaperone-mediated histone acetylation


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 
    0.248 (Depositor), 0.258 (DCC) 
  • R-Value Work: 
    0.207 (Depositor), 0.215 (DCC) 
  • R-Value Observed: 
    0.209 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.5 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 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.

Macromolecule Content 

  • Total Structure Weight: 78.51 kDa 
  • Atom Count: 5,040 
  • Modeled Residue Count: 607 
  • Deposited Residue Count: 670 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Histone acetyltransferase438Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: KIM2L1377REM50RTT109YLL002W
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
Find similar proteins by:|  3D Structure
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
Expand
Reference Sequence

Small Molecules

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: 3.30 Å
  • R-Value Free:  0.248 (Depositor), 0.258 (DCC) 
  • R-Value Work:  0.207 (Depositor), 0.215 (DCC) 
  • R-Value Observed: 0.209 (Depositor) 
Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 98.085α = 90
b = 119.001β = 90
c = 80.292γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
AMoREphasing
CNSrefinement
HKL-2000data reduction
SCALEPACKdata scaling
Blu-Icedata collection

Structure Validation

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Ligand Structure Quality Assessment 


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: 2019-07-17
    Changes: Data collection, Derived calculations, Refinement description
  • Version 1.3: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.4: 2023-12-06
    Changes: Data collection
  • Version 1.5: 2024-11-06
    Changes: Structure summary