6KBB

Role of the DEF/Y motif of Swc5 in histone H2A.Z deposition


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.37 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.189 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Role of a DEF/Y motif in histone H2A-H2B recognition and nucleosome editing.

Huang, Y.Sun, L.Pierrakeas, L.Dai, L.Pan, L.Luk, E.Zhou, Z.

(2020) Proc Natl Acad Sci U S A 117: 3543-3550

  • DOI: https://doi.org/10.1073/pnas.1914313117
  • Primary Citation of Related Structures:  
    6KBB

  • PubMed Abstract: 

    The SWR complex edits the histone composition of nucleosomes at promoters to facilitate transcription by replacing the two nucleosomal H2A-H2B (A-B) dimers with H2A.Z-H2B (Z-B) dimers. Swc5, a subunit of SWR, binds to A-B dimers, but its role in the histone replacement reaction was unclear. In this study, we showed that Swc5 uses a tandem DEF/Y motif within an intrinsically disordered region to engage the A-B dimer. A 2.37-Å X-ray crystal structure of the histone binding domain of Swc5 in complex with an A-B dimer showed that consecutive acidic residues and flanking hydrophobic residues of Swc5 form a cap over the histones, excluding histone-DNA interaction. Mutations in Swc5 DEF/Y inhibited the nucleosome editing function of SWR in vitro. Swc5 DEF/Y interacts with histones in vivo, and the extent of this interaction is dependent on the remodeling ATPase of SWR, supporting a model in which Swc5 acts as a wedge to promote A-B dimer eviction. Given that DEF/Y motifs are found in other evolutionary unrelated chromatin regulators, this work provides the molecular basis for a general strategy used repeatedly during eukaryotic evolution to mobilize histones in various genomic functions.


  • Organizational Affiliation

    Department of Biochemistry and Cell Biology, Stony Brook University, NY 11794-5215; ed.luk@stonybrook.edu zhouzh@ibp.ac.cn.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2A type 1-DA [auth C],
D [auth A]
96Homo sapiensMutation(s): 0 
Gene Names: HIST1H2ADH2AFG
UniProt & NIH Common Fund Data Resources
Find proteins for P20671 (Homo sapiens)
Explore P20671 
Go to UniProtKB:  P20671
PHAROS:  P20671
GTEx:  ENSG00000196866 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP20671
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2B type 2-EB [auth D],
E [auth B]
104Homo sapiensMutation(s): 0 
Gene Names: HIST2H2BEH2BFQ
UniProt & NIH Common Fund Data Resources
Find proteins for Q16778 (Homo sapiens)
Explore Q16778 
Go to UniProtKB:  Q16778
PHAROS:  Q16778
GTEx:  ENSG00000184678 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ16778
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
SWR1-complex protein 5C [auth F],
F [auth E]
81Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SWC5AOR1YBR231CYBR1529
UniProt
Find proteins for P38326 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P38326 
Go to UniProtKB:  P38326
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP38326
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.37 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.189 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 107.072α = 90
b = 65.521β = 122.83
c = 84.821γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (China)China--

Revision History  (Full details and data files)

  • Version 1.0: 2020-01-29
    Type: Initial release
  • Version 1.1: 2020-02-19
    Changes: Database references
  • Version 1.2: 2020-03-04
    Changes: Database references
  • Version 1.3: 2023-11-22
    Changes: Data collection, Database references, Refinement description