4M6B

Crystal structure of yeast Swr1-Z domain in complex with H2A.Z-H2B dimer


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.78 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.226 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

The Catalytic Subunit of the SWR1 Remodeler Is a Histone Chaperone for the H2A.Z-H2B Dimer.

Hong, J.Feng, H.Wang, F.Ranjan, A.Chen, J.Jiang, J.Ghirlando, R.Xiao, T.S.Wu, C.Bai, Y.

(2014) Mol Cell 53: 498-505

  • DOI: 10.1016/j.molcel.2014.01.010
  • Primary Citation of Related Structures:  
    4M6B

  • PubMed Abstract: 
  • Histone variant H2A.Z-containing nucleosomes exist at most eukaryotic promoters and play important roles in gene transcription and genome stability. The multisubunit nucleosome-remodeling enzyme complex SWR1, conserved from yeast to mammals, catalyze ...

    Histone variant H2A.Z-containing nucleosomes exist at most eukaryotic promoters and play important roles in gene transcription and genome stability. The multisubunit nucleosome-remodeling enzyme complex SWR1, conserved from yeast to mammals, catalyzes the ATP-dependent replacement of histone H2A in canonical nucleosomes with H2A.Z. How SWR1 catalyzes the replacement reaction is largely unknown. Here, we determined the crystal structure of the N-terminal region (599-627) of the catalytic subunit Swr1, termed Swr1-Z domain, in complex with the H2A.Z-H2B dimer at 1.78 Å resolution. The Swr1-Z domain forms a 310 helix and an irregular chain. A conserved LxxLF motif in the Swr1-Z 310 helix specifically recognizes the αC helix of H2A.Z. Our results show that the Swr1-Z domain can deliver the H2A.Z-H2B dimer to the DNA-(H3-H4)2 tetrasome to form the nucleosome by a histone chaperone mechanism.


    Organizational Affiliation

    Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, NIH, Bethesda, MD 20892, USA. Electronic address: yawen@helix.nih.gov.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Chimera protein of Histone H2B.1 and Histone H2A.ZAD193Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: HTB1H2B1SPT12YDR224CYD9934.09CHTZ1H2AZHTA3YOL012CO2345
Find proteins for P02293 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Go to UniProtKB:  P02293
Find proteins for Q12692 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q12692 
Go to UniProtKB:  Q12692
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Helicase SWR1CF55Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SWR1YDR334WD9651.6
EC: 3.6.4.12
Find proteins for Q05471 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q05471 
Go to UniProtKB:  Q05471
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.78 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.226 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.667α = 90
b = 69.917β = 90
c = 101.724γ = 90
Software Package:
Software NamePurpose
Blu-Icedata collection
PHASERphasing
CNSrefinement
XDSdata reduction
XDSdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-02-19
    Type: Initial release
  • Version 1.1: 2016-01-13
    Changes: Structure summary
  • Version 1.2: 2017-07-26
    Changes: Refinement description, Source and taxonomy
  • Version 1.3: 2017-11-15
    Changes: Refinement description