3Q68

Structure of the Vps75-Rtt109 histone chaperone-lysine acetyltransferase complex (Full-length proteins in space group P212121)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.71 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.202 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structure and histone binding properties of the Vps75-Rtt109 chaperone-lysine acetyltransferase complex.

Su, D.Hu, Q.Zhou, H.Thompson, J.R.Xu, R.M.Zhang, Z.Mer, G.

(2011) J Biol Chem 286: 15625-15629

  • DOI: https://doi.org/10.1074/jbc.C111.220715
  • Primary Citation of Related Structures:  
    3Q66, 3Q68

  • PubMed Abstract: 

    The histone chaperone Vps75 presents the remarkable property of stimulating the Rtt109-dependent acetylation of several histone H3 lysine residues within (H3-H4)(2) tetramers. To investigate this activation mechanism, we determined x-ray structures of full-length Vps75 in complex with full-length Rtt109 in two crystal forms. Both structures show similar asymmetric assemblies of a Vps75 dimer bound to an Rtt109 monomer. In the Vps75-Rtt109 complexes, the catalytic site of Rtt109 is confined to an enclosed space that can accommodate the N-terminal tail of histone H3 in (H3-H4)(2). Investigation of Vps75-Rtt109-(H3-H4)(2) and Vps75-(H3-H4)(2) complexes by NMR spectroscopy-probed hydrogen/deuterium exchange suggests that Vps75 guides histone H3 in the catalytic enclosure. These findings clarify the basis for the enhanced acetylation of histone H3 tail residues by Vps75-Rtt109.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Vacuolar protein sorting-associated protein 75 (VPS75)A,
C [auth B]
264Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: VPS75YNL246WN0890
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
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Histone acetyltransferase RTT109B [auth C]442Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: RTT109KIM2REM50YLL002WL1377
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
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
ALY
Query on ALY
B [auth C]L-PEPTIDE LINKINGC8 H16 N2 O3LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.71 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.202 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 90.988α = 90
b = 98.056β = 90
c = 171.366γ = 90
Software Package:
Software NamePurpose
HKL-3000data collection
PHASERphasing
PHENIXrefinement
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: 2011-03-23
    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