7D1Z

Cryo-EM structure of SET8-nucleosome complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.15 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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Literature

Structural basis of nucleosomal histone H4 lysine 20 methylation by SET8 methyltransferase.

Ho, C.H.Takizawa, Y.Kobayashi, W.Arimura, Y.Kimura, H.Kurumizaka, H.

(2021) Life Sci Alliance 4

  • DOI: 10.26508/lsa.202000919
  • Primary Citation of Related Structures:  
    7D1Z, 7D20

  • PubMed Abstract: 
  • SET8 is solely responsible for histone H4 lysine-20 (H4K20) monomethylation, which preferentially occurs in nucleosomal H4. However, the underlying mechanism by which SET8 specifically promotes the H4K20 monomethylation in the nucleosome has not been elucidated ...

    SET8 is solely responsible for histone H4 lysine-20 (H4K20) monomethylation, which preferentially occurs in nucleosomal H4. However, the underlying mechanism by which SET8 specifically promotes the H4K20 monomethylation in the nucleosome has not been elucidated. Here, we report the cryo-EM structures of the human SET8-nucleosome complexes with histone H3 and the centromeric H3 variant, CENP-A. Surprisingly, we found that the overall cryo-EM structures of the SET8-nucleosome complexes are substantially different from the previous crystal structure models. In the complexes with H3 and CENP-A nucleosomes, SET8 specifically binds the nucleosomal acidic patch via an arginine anchor, composed of the Arg188 and Arg192 residues. Mutational analyses revealed that the interaction between the SET8 arginine anchor and the nucleosomal acidic patch plays an essential role in the H4K20 monomethylation activity. These results provide the groundwork for understanding the mechanism by which SET8 specifically accomplishes the H4K20 monomethylation in the nucleosome.


    Organizational Affiliation

    Graduate School of Advanced Science and Engineering, Waseda University, Tokyo, Japan.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H3.1A, E139Homo sapiensMutation(s): 0 
Gene Names: 
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Find proteins for P68431 (Homo sapiens)
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PHAROS:  P68431
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UniProt GroupP68431
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H4B,
K [auth F]
106Homo sapiensMutation(s): 0 
Gene Names: 
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Find proteins for P62805 (Homo sapiens)
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UniProt GroupP62805
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H2A type 1-B/EC,
F [auth G]
133Homo sapiensMutation(s): 0 
Gene Names: H2AC4H2AFMHIST1H2ABH2AC8H2AFAHIST1H2AE
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Find proteins for P04908 (Homo sapiens)
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H2B type 1-JD,
G [auth H]
129Homo sapiensMutation(s): 0 
Gene Names: H2BC11H2BFRHIST1H2BJ
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Find proteins for P06899 (Homo sapiens)
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GTEx:  ENSG00000124635 
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Isoform 2 of N-lysine methyltransferase KMT5AJ [auth K]352Homo sapiensMutation(s): 0 
Gene Names: KMT5APRSET7SET07SET8SETD8
EC: 2.1.1 (PDB Primary Data), 2.1.1.361 (PDB Primary Data)
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GTEx:  ENSG00000183955 
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Entity ID: 5
MoleculeChainsLengthOrganismImage
DNA (145-MER)H [auth I]145synthetic construct
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Entity ID: 6
MoleculeChainsLengthOrganismImage
DNA (145-MER)I [auth J]145synthetic construct
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.15 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)JapanJP17H01408
Japan Society for the Promotion of Science (JSPS)JapanJP18H05534
Japan Society for the Promotion of Science (JSPS)JapanJP19K06522
Japan Science and TechnologyJapanJPMJCR16G1
Japan Agency for Medical Research and Development (AMED)JapanJP19am0101076
Japan Science and TechnologyJapanJPMJER1901

Revision History  (Full details and data files)

  • Version 1.0: 2021-02-10
    Type: Initial release
  • Version 1.1: 2021-03-03
    Changes: Database references