3C9D | pdb_00003c9d

Crystal structure of Vps75


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 
    0.251 (Depositor), 0.257 (DCC) 
  • R-Value Work: 
    0.229 (Depositor), 0.235 (DCC) 
  • R-Value Observed: 
    0.230 (Depositor) 

wwPDB Validation 3D Report Full Report

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This is version 1.3 of the entry. See complete history

Literature

Molecular functions of the histone acetyltransferase chaperone complex Rtt109-Vps75

Berndsen, C.E.Tsubota, T.Lindner, S.E.Lee, S.Holton, J.M.Kaufman, P.D.Keck, J.L.Denu, J.M.

(2008) Nat Struct Mol Biol 15: 948-956

  • DOI: https://doi.org/10.1038/nsmb.1459
  • Primary Citation Related Structures: 
    3C9B, 3C9D

  • PubMed Abstract: 

    Histone acetylation and nucleosome remodeling regulate DNA damage repair, replication and transcription. Rtt109, a recently discovered histone acetyltransferase (HAT) from Saccharomyces cerevisiae, functions with the histone chaperone Asf1 to acetylate lysine K56 on histone H3 (H3K56), a modification associated with newly synthesized histones. In vitro analysis of Rtt109 revealed that Vps75, a Nap1 family histone chaperone, could also stimulate Rtt109-dependent acetylation of H3K56. However, the molecular function of the Rtt109-Vps75 complex remains elusive. Here we have probed the molecular functions of Vps75 and the Rtt109-Vps75 complex through biochemical, structural and genetic means. We find that Vps75 stimulates the kcat of histone acetylation by approximately 100-fold relative to Rtt109 alone and enhances acetylation of K9 in the H3 histone tail. Consistent with the in vitro evidence, cells lacking Vps75 showed a substantial reduction (60%) in H3K9 acetylation during S phase. X-ray structural, biochemical and genetic analyses of Vps75 indicate a unique, structurally dynamic Nap1-like fold that suggests a potential mechanism of Vps75-dependent activation of Rttl09. Together, these data provide evidence for a multifunctional HAT-chaperone complex that acetylates histone H3 and deposits H3-H4 onto DNA, linking histone modification and nucleosome assembly.


  • Organizational Affiliation
    • Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, 1300 University Avenue, Madison, Wisconsin 53706, USA.

Macromolecule Content 

  • Total Structure Weight: 60.02 kDa 
  • Atom Count: 3,761 
  • Modeled Residue Count: 413 
  • Deposited Residue Count: 518 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Vacuolar protein sorting-associated protein 75
A, B
259Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: VPS75
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

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free:  0.251 (Depositor), 0.257 (DCC) 
  • R-Value Work:  0.229 (Depositor), 0.235 (DCC) 
  • R-Value Observed: 0.230 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.805α = 90
b = 86.085β = 90
c = 85.641γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-08-12
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Refinement description, Version format compliance
  • Version 1.2: 2017-10-25
    Changes: Refinement description
  • Version 1.3: 2024-02-21
    Changes: Data collection, Database references