4M6B | pdb_00004m6b

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 (Depositor), 0.220 (DCC) 
  • R-Value Work: 
    0.211 (Depositor), 0.211 (DCC) 
  • R-Value Observed: 
    0.226 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 4M6B

This is version 1.4 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: https://doi.org/10.1016/j.molcel.2014.01.010
  • Primary Citation 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, 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.

Macromolecule Content 

  • Total Structure Weight: 54.35 kDa 
  • Atom Count: 3,398 
  • Modeled Residue Count: 418 
  • Deposited Residue Count: 496 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Chimera protein of Histone H2B.1 and Histone H2A.ZA,
C [auth D]
193Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: HTB1H2B1SPT12YDR224CYD9934.09CHTZ1H2AZHTA3YOL012CO2345
UniProt
Find proteins for P02293 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P02293 
Go to UniProtKB:  P02293
Find proteins for Q12692 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q12692 
Go to UniProtKB:  Q12692
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsQ12692P02293
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Helicase SWR1B [auth C],
D [auth F]
55Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SWR1YDR334WD9651.6
EC: 3.6.4.12 (PDB Primary Data), 3.6.4 (UniProt)
UniProt
Find proteins for Q05471 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q05471 
Go to UniProtKB:  Q05471
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ05471
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.78 Å
  • R-Value Free:  0.220 (Depositor), 0.220 (DCC) 
  • R-Value Work:  0.211 (Depositor), 0.211 (DCC) 
  • R-Value Observed: 0.226 (Depositor) 
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

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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
  • Version 1.4: 2024-02-28
    Changes: Data collection, Database references