7DLX

crystal structure of H2AM4>Z-H2B


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.229 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Recognition of the inherently unstable H2A nucleosome by Swc2 is a major determinant for unidirectional H2A.Z exchange.

Dai, L.Xiao, X.Pan, L.Shi, L.Xu, N.Zhang, Z.Feng, X.Ma, L.Dou, S.Wang, P.Zhu, B.Li, W.Zhou, Z.

(2021) Cell Rep 35: 109183-109183

  • DOI: 10.1016/j.celrep.2021.109183
  • Primary Citation of Related Structures:  
    7DLX

  • PubMed Abstract: 
  • The multisubunit chromatin remodeler SWR1/SRCAP/p400 replaces the nucleosomal H2A-H2B dimer with the free-form H2A.Z-H2B dimer, but the mechanism governing the unidirectional H2A-to-H2A.Z exchange remains elusive. Here, we perform single-molecule force spectroscopy to dissect the disassembly/reassembly processes of the H2A nucleosome and H2A ...

    The multisubunit chromatin remodeler SWR1/SRCAP/p400 replaces the nucleosomal H2A-H2B dimer with the free-form H2A.Z-H2B dimer, but the mechanism governing the unidirectional H2A-to-H2A.Z exchange remains elusive. Here, we perform single-molecule force spectroscopy to dissect the disassembly/reassembly processes of the H2A nucleosome and H2A.Z nucleosome. We find that the N-terminal 1-135 residues of yeast SWR1 complex protein 2 (previously termed Swc2-Z) facilitate the disassembly of nucleosomes containing H2A but not H2A.Z. The Swc2-mediated nucleosome disassembly/reassembly requires the inherently unstable H2A nucleosome, whose instability is conferred by three H2A α2-helical residues, Gly47, Pro49, and Ile63, as they selectively weaken the structural rigidity of the H2A-H2B dimer. It also requires Swc2-ZN (residues 1-37) that directly anchors to the H2A nucleosome and functions in the SWR1-catalyzed H2A.Z replacement in vitro and yeast H2A.Z deposition in vivo. Our findings provide mechanistic insights into how the SWR1 complex discriminates between the H2A nucleosome and H2A.Z nucleosome, establishing a simple paradigm for the governance of unidirectional H2A.Z exchange.


    Organizational Affiliation

    National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China. Electronic address: zhouzh@ibp.ac.cn.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H2B,Histone H2A
A, B, C, D, E, F, G, H
A, B, C, D, E, F, G, H
208Saccharomyces cerevisiae RM11-1aMutation(s): 5 
Gene Names: SCRG_00300SCRG_00299
UniProt
Find proteins for P02293 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P02293 
Go to UniProtKB:  P02293
Find proteins for P04911 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P04911 
Go to UniProtKB:  P04911
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP04911P02293
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.229 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 102.582α = 90
b = 73.237β = 95.48
c = 109.682γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

View Full Validation Report




Entry History & Funding Information

Deposition Data

  • Deposited Date: 2020-11-30 
  • Released Date: 2021-06-16 
  • Deposition Author(s): Dai, L.C., Zhou, Z.

Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China32000421, 21991133, 11874414, 31770812, 11774407, 11874415, 31970621, 31871318, 31801070

Revision History  (Full details and data files)

  • Version 1.0: 2021-06-16
    Type: Initial release