4AM7

ADP-BOUND C-TERMINAL DOMAIN OF ACTIN-RELATED PROTEIN ARP8 FROM S. CEREVISIAE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.25 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.223 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Interactions between the Nucleosome Histone Core and Arp8 in the Ino80 Chromatin Remodeling Complex.

Saravanan, M.Wuerges, J.Bose, D.Mccormack, E.A.Cook, N.J.Zhang, X.Wigley, D.B.

(2012) Proc Natl Acad Sci U S A 109: 20883

  • DOI: https://doi.org/10.1073/pnas.1214735109
  • Primary Citation of Related Structures:  
    4AM6, 4AM7

  • PubMed Abstract: 

    Actin-related protein Arp8 is a component of the INO80 chromatin remodeling complex. Yeast Arp8 (yArp8) comprises two domains: a 25-KDa N-terminal domain, found only in yeast, and a 75-KDa C-terminal domain (yArp8CTD) that contains the actin fold and is conserved across other species. The crystal structure shows that yArp8CTD contains three insertions within the actin core. Using a combination of biochemistry and EM, we show that Arp8 forms a complex with nucleosomes, and that the principal interactions are via the H3 and H4 histones, mediated through one of the yArp8 insertions. We show that recombinant yArp8 exists in monomeric and dimeric states, but the dimer is the biologically relevant form required for stable interactions with histones that exploits the twofold symmetry of the nucleosome core. Taken together, these data provide unique insight into the stoichiometry, architecture, and molecular interactions between components of the INO80 remodeling complex and nucleosomes, providing a first step toward building up the structure of the complex.


  • Organizational Affiliation

    Chester Beatty Laboratories, Institute of Cancer Research, London SW3 6JB, United Kingdom.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ACTIN-LIKE PROTEIN ARP8
A, B
655Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for Q12386 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q12386 
Go to UniProtKB:  Q12386
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ12386
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.25 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.223 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 137.718α = 90
b = 89.795β = 114.37
c = 149.647γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-12-12
    Type: Initial release
  • Version 1.1: 2013-01-16
    Changes: Database references
  • Version 1.2: 2019-11-13
    Changes: Data collection, Database references, Other
  • Version 1.3: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Refinement description