7YBF | pdb_00007ybf

Crystal structure of inner membrane protein Sad1 in complex with histone H2A-H2B


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 
    0.248 (Depositor), 0.250 (DCC) 
  • R-Value Work: 
    0.198 (Depositor), 0.200 (DCC) 
  • R-Value Observed: 
    0.203 (Depositor) 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

The SUN-family protein Sad1 mediates heterochromatin spatial organization through interaction with histone H2A-H2B.

Sun, W.Dong, Q.Li, X.Gao, J.Ye, X.Hu, C.Li, F.Chen, Y.

(2024) Nat Commun 15: 4322-4322

  • DOI: https://doi.org/10.1038/s41467-024-48418-7
  • Primary Citation of Related Structures:  
    7YBF

  • PubMed Abstract: 

    Heterochromatin is generally associated with the nuclear periphery, but how the spatial organization of heterochromatin is regulated to ensure epigenetic silencing remains unclear. Here we found that Sad1, an inner nuclear membrane SUN-family protein in fission yeast, interacts with histone H2A-H2B but not H3-H4. We solved the crystal structure of the histone binding motif (HBM) of Sad1 in complex with H2A-H2B, revealing the intimate contacts between Sad1 HBM and H2A-H2B. Structure-based mutagenesis studies revealed that the H2A-H2B-binding activity of Sad1 is required for the dynamic distribution of Sad1 throughout the nuclear envelope (NE). The Sad1-H2A-H2B complex mediates tethering telomeres and the mating-type locus to the NE. This complex is also important for heterochromatin silencing. Mechanistically, H2A-H2B enhances the interaction between Sad1 and HDACs, including Clr3 and Sir2, to maintain epigenetic identity of heterochromatin. Interestingly, our results suggest that Sad1 exhibits the histone-enhanced liquid-liquid phase separation property, which helps recruit heterochromatin factors to the NE. Our results uncover an unexpected role of SUN-family proteins in heterochromatin regulation and suggest a nucleosome-independent role of H2A-H2B in regulating Sad1's functionality.


  • Organizational Affiliation

    State Key Laboratory of Molecular Biology, Key Laboratory of Epigenetic Regulation and Intervention, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2B-alpha,Histone H2A-beta
A, B
189Schizosaccharomyces pombeMutation(s): 0 
Gene Names: htb1SPCC622.09hta2SPAC19G12.06c
UniProt
Find proteins for P04910 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Explore P04910 
Go to UniProtKB:  P04910
Find proteins for P04913 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Explore P04913 
Go to UniProtKB:  P04913
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP04913P04910
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Spindle pole body-associated protein sad117Schizosaccharomyces pombeMutation(s): 0 
Gene Names: sad1SPBC12D12.01SPBC16H5.01c
UniProt
Find proteins for Q09825 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Explore Q09825 
Go to UniProtKB:  Q09825
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ09825
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free:  0.248 (Depositor), 0.250 (DCC) 
  • R-Value Work:  0.198 (Depositor), 0.200 (DCC) 
  • R-Value Observed: 0.203 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.804α = 90
b = 61.981β = 101.89
c = 76.016γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Chinese Academy of SciencesChinaXDB37010303

Revision History  (Full details and data files)

  • Version 1.0: 2024-01-03
    Type: Initial release
  • Version 1.1: 2024-07-17
    Changes: Database references