6M2M

A role for histone chaperone OsChz1 in histone recognition and deposition


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.196 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

OsChz1 acts as a histone chaperone in modulating chromatin organization and genome function in rice.

Du, K.Luo, Q.Yin, L.Wu, J.Liu, Y.Gan, J.Dong, A.Shen, W.H.

(2020) Nat Commun 11: 5717-5717

  • DOI: https://doi.org/10.1038/s41467-020-19586-z
  • Primary Citation of Related Structures:  
    6M2M

  • PubMed Abstract: 

    While the yeast Chz1 acts as a specific histone-chaperone for H2A.Z, functions of CHZ-domain proteins in multicellular eukaryotes remain obscure. Here, we report on the functional characterization of OsChz1, a sole CHZ-domain protein identified in rice. OsChz1 interacts with both the canonical H2A-H2B dimer and the variant H2A.Z-H2B dimer. Within crystal structure the C-terminal region of OsChz1 binds H2A-H2B via an acidic region, pointing to a previously unknown recognition mechanism. Knockout of OsChz1 leads to multiple plant developmental defects. At genome-wide level, loss of OsChz1 causes mis-regulations of thousands of genes and broad alterations of nucleosome occupancy as well as reductions of H2A.Z-enrichment. While OsChz1 associates with chromatin regions enriched of repressive histone marks (H3K27me3 and H3K4me2), its loss does not affect the genome landscape of DNA methylation. Taken together, it is emerging that OsChz1 functions as an important H2A/H2A.Z-H2B chaperone in dynamic regulation of chromatin for higher eukaryote development.


  • Organizational Affiliation

    State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, International Associated Laboratory of CNRS-Fudan-HUNAU on Plant Epigenome Research, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Probable histone H2A.393Arabidopsis thalianaMutation(s): 0 
Gene Names: At4g27230M4I22.40
UniProt
Find proteins for O81826 (Arabidopsis thaliana)
Explore O81826 
Go to UniProtKB:  O81826
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO81826
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2B.198Arabidopsis thalianaMutation(s): 0 
Gene Names: At1g07790F24B9.10
UniProt
Find proteins for Q9LQQ4 (Arabidopsis thaliana)
Explore Q9LQQ4 
Go to UniProtKB:  Q9LQQ4
Entity Groups  
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UniProt GroupQ9LQQ4
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Expressed protein
M, N, O
105Oryza sativa Japonica GroupMutation(s): 0 
Gene Names: LOC_Os11g34190Os11g0544600OSNPB_110544600
UniProt
Find proteins for Q2R2Z3 (Oryza sativa subsp. japonica)
Explore Q2R2Z3 
Go to UniProtKB:  Q2R2Z3
Entity Groups  
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UniProt GroupQ2R2Z3
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.196 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 167.361α = 90
b = 116.336β = 114.98
c = 101.904γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction
REFMACphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-10-21
    Type: Initial release
  • Version 1.1: 2020-11-25
    Changes: Database references
  • Version 1.2: 2024-03-27
    Changes: Data collection, Database references