3Q66

Structure of the Vps75-Rtt109 histone chaperone-lysine acetyltransferase complex (Full-length proteins in space group P6122)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.705 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.206 

wwPDB Validation 3D Report Full Report


This is version 1.1 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: 10.1074/jbc.C111.220715
  • Primary Citation of Related Structures:  

  • 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 o ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Vacuolar protein sorting-associated protein 75
A, B
264Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: VPS75
Find proteins for P53853 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P53853
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Histone acetyltransferase RTT109
C
442Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RTT109 (KIM2, REM50)
EC: 2.3.1.48
Find proteins for Q07794 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q07794
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, C
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
ALY
Query on ALY
C
L-PEPTIDE LINKINGC8 H16 N2 O3LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.705 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.206 
  • Space Group: P 61 2 2
Unit Cell:
Length (Å)Angle (°)
a = 99.385α = 90.00
b = 99.385β = 90.00
c = 479.605γ = 120.00
Software Package:
Software NamePurpose
PHASERphasing
HKL-3000data scaling
HKL-3000data collection
HKL-3000data reduction
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-03-23
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance