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 

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

  • 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 Immunology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA.,Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda, MD 20892, USA.,Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, NIH, Bethesda, MD 20892, USA. Electronic address: yawen@helix.nih.gov.,Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, NIH, Bethesda, MD 20892, USA; Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA.,Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, NIH, Bethesda, MD 20892, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Chimera protein of Histone H2B.1 and Histone H2A.Z
A, D
193Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: HTZ1 (H2AZ, HTA3), HTB1 (H2B1, SPT12)
Find proteins for Q12692 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q12692
Find proteins for P02293 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P02293
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Helicase SWR1
C, F
55Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: SWR1
EC: 3.6.4.12
Find proteins for Q05471 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q05471
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.78 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.211 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 65.667α = 90.00
b = 69.917β = 90.00
c = 101.724γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
XDSdata reduction
CNSrefinement
Blu-Icedata collection
XDSdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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