5AGC | pdb_00005agc

Crystallographic forms of the Vps75 tetramer


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.00 Å
  • R-Value Free: 
    0.265 (Depositor), 0.252 (DCC) 
  • R-Value Work: 
    0.229 (Depositor), 0.245 (DCC) 
  • R-Value Observed: 
    0.231 (Depositor) 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history

Literature

The Histone Chaperone Vps75 Forms Multiple Oligomeric Assemblies Capable of Mediating Exchange between Histone H3-H4 Tetramers and Asf1-H3-H4 Complexes.

Hammond, C.M.Sundaramoorthy, R.Larance, M.Lamond, A.Stevens, M.A.El-Mkami, H.Norman, D.G.Owen-Hughes, T.

(2016) Nucleic Acids Res 44: 6157

  • DOI: https://doi.org/10.1093/nar/gkw209
  • Primary Citation Related Structures: 
    5AGC

  • PubMed Abstract: 

    Vps75 is a histone chaperone that has been historically characterized as homodimer by X-ray crystallography. In this study, we present a crystal structure containing two related tetrameric forms of Vps75 within the crystal lattice. We show Vps75 associates with histones in multiple oligomers. In the presence of equimolar H3-H4 and Vps75, the major species is a reconfigured Vps75 tetramer bound to a histone H3-H4 tetramer. However, in the presence of excess histones, a Vps75 dimer bound to a histone H3-H4 tetramer predominates. We show the Vps75-H3-H4 interaction is compatible with the histone chaperone Asf1 and deduce a structural model of the Vps75-Asf1-H3-H4 (VAH) co-chaperone complex using the Pulsed Electron-electron Double Resonance (PELDOR) technique and cross-linking MS/MS distance restraints. The model provides a molecular basis for the involvement of both Vps75 and Asf1 in Rtt109 catalysed histone H3 K9 acetylation. In the absence of Asf1 this model can be used to generate a complex consisting of a reconfigured Vps75 tetramer bound to a H3-H4 tetramer. This provides a structural explanation for many of the complexes detected biochemically and illustrates the ability of Vps75 to interact with dimeric or tetrameric H3-H4 using the same interaction surface.


  • Organizational Affiliation
    • Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK.

Macromolecule Content 

  • Total Structure Weight: 122.62 kDa 
  • Atom Count: 7,250 
  • Modeled Residue Count: 869 
  • Deposited Residue Count: 1,056 
  • 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, C, D
264Saccharomyces cerevisiaeMutation(s): 0 
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: 4.00 Å
  • R-Value Free:  0.265 (Depositor), 0.252 (DCC) 
  • R-Value Work:  0.229 (Depositor), 0.245 (DCC) 
  • R-Value Observed: 0.231 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.75α = 90
b = 92.43β = 93.85
c = 160.75γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-03-02
    Type: Initial release
  • Version 1.1: 2016-04-13
    Changes: Database references
  • Version 1.2: 2016-08-10
    Changes: Database references
  • Version 1.3: 2024-01-10
    Changes: Data collection, Database references, Other, Refinement description