8JHF

Native SUV420H1 bound to 167-bp nucleosome


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.68 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural basis of nucleosomal H4K20 recognition and methylation by SUV420H1 methyltransferase.

Lin, F.Zhang, R.Shao, W.Lei, C.Ma, M.Zhang, Y.Wen, Z.Li, W.

(2023) Cell Discov 9: 120-120

  • DOI: https://doi.org/10.1038/s41421-023-00620-5
  • Primary Citation of Related Structures:  
    8JHF, 8JHG

  • PubMed Abstract: 

    Histone lysine methyltransferase SUV420H1, which is responsible for site-specific di-/tri-methylation of histone H4 lysine 20 (H4K20), has crucial roles in DNA-templated processes, including DNA replication, DNA damage repair, and chromatin compaction. Its mutations frequently occur in human cancers. Nucleosomes containing the histone variant H2A.Z enhance the catalytic activities of SUV420H1 on H4K20 di-methylation deposition, regulating early replication origins. However, the molecular mechanism by which SUV420H1 specifically recognizes and deposits H4K20 methyl marks on nucleosomes remains poorly understood. Here we report the cryo-electron microscopy structures of SUV420H1 associated with H2A-containing nucleosome core particles (NCPs), and H2A.Z-containing NCPs. We find that SUV420H1 makes extensive site-specific contacts with histone and DNA regions. SUV420H1 C-terminal domain recognizes the H2A-H2B acidic patch of NCPs through its two arginine anchors, thus enabling H4K20 insertion for catalysis specifically. We also identify important residues increasing the catalytic activities of SUV420H1 bound to H2A.Z NCPs. In vitro and in vivo functional analyses reveal that multiple disease-associated mutations at the interfaces are essential for its catalytic activity and chromatin state regulation. Together, our study provides molecular insights into the nucleosome-based recognition and methylation mechanisms of SUV420H1, and a structural basis for understanding SUV420H1-related human disease.


  • Organizational Affiliation

    Department of Pharmacology, Joint Laboratory of Guangdong-Hong Kong Universities for Vascular Homeostasis and Diseases, School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong, China.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Histone-lysine N-methyltransferase KMT5BA [auth K]361Homo sapiensMutation(s): 0 
Gene Names: KMT5BSUV420H1CGI-85
EC: 2.1.1.362 (PDB Primary Data), 2.1.1.361 (PDB Primary Data)
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Find proteins for Q4FZB7 (Homo sapiens)
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Go to UniProtKB:  Q4FZB7
PHAROS:  Q4FZB7
GTEx:  ENSG00000110066 
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UniProt GroupQ4FZB7
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H3.1B [auth A],
F [auth E]
136Homo sapiensMutation(s): 0 
Gene Names: 
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Find proteins for P68431 (Homo sapiens)
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UniProt GroupP68431
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H4C [auth B],
G [auth F]
86Homo sapiensMutation(s): 1 
Gene Names: 
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Find proteins for P62805 (Homo sapiens)
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UniProt GroupP62805
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2A.ZD [auth C],
H [auth G]
113Homo sapiensMutation(s): 0 
Gene Names: H2AZ1H2AFZH2AZ
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Find proteins for P0C0S5 (Homo sapiens)
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GTEx:  ENSG00000164032 
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UniProt GroupP0C0S5
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2B type 1-KE [auth D],
I [auth H]
95Homo sapiensMutation(s): 0 
Gene Names: H2BC12H2BFTHIRIP1HIST1H2BK
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Find proteins for O60814 (Homo sapiens)
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PHAROS:  O60814
GTEx:  ENSG00000197903 
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Entity ID: 6
MoleculeChains LengthOrganismImage
DNA (160-MER)J [auth I]160Homo sapiens
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Entity ID: 7
MoleculeChains LengthOrganismImage
DNA (160-MER)K [auth J]160Homo sapiens
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.68 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data

  • Released Date: 2023-11-15 
  • Deposition Author(s): Lin, F., Li, W.

Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China32200473

Revision History  (Full details and data files)

  • Version 1.0: 2023-11-15
    Type: Initial release
  • Version 1.1: 2023-12-20
    Changes: Database references