Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 9-mer - A2B2C2D2E1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 9-mer - A5B3C1 Local Symmetry: Cyclic - C2  (3D View)
Local Stoichiometry: Hetero 8-mer - A2B2C2D2 

Local Symmetry: Cyclic - C2  (3D View)
Local Stoichiometry: Hetero 8-mer - A2B2C2D2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: native gel electrophoresis

Macromolecule Content

• Total Structure Weight: 242.1 kDa 
• Atom Count: 12,836 
• Modelled Residue Count: 1,186 
• Deposited Residue Count: 1,664 
• Unique protein chains: 5
• Unique nucleic acid chains: 2

 7D20

Cryo-EM structure of SET8-CENP-A-nucleosome complex

• PDB DOI:  https://doi.org/10.2210/pdb7D20/pdb
• EM Map EMD-30552: EMDB EMDataResource

• Classification: NUCLEAR PROTEIN
• Organism(s): Homo sapiens, synthetic construct
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2020-09-15 Released: 2021-02-10 
• Deposition Author(s): Ho, C.-H., Takizawa, Y., Kobayashi, W., Arimura, Y., Kurumizaka, H.
• Funding Organization(s): Japan Society for the Promotion of Science (JSPS), Japan Science and Technology, Japan Agency for Medical Research and Development (AMED)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.00 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

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

• PubMed: 33574035 
• DOI: https://doi.org/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. 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H3-like centromeric protein A	A, B [auth E]	143	Homo sapiens	Mutation(s): 0  Gene Names: CENPA
UniProt & NIH Common Fund Data Resources
Find proteins for P49450 (Homo sapiens) Explore P49450  Go to UniProtKB:  P49450
PHAROS:  P49450

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H4	C [auth B], F	106	Homo sapiens	Mutation(s): 0  Gene Names:  H4C1, H4/A, H4FA, HIST1H4A, H4C2, H4/I, H4FI, HIST1H4B, H4C3, H4/G, H4FG, HIST1H4C, H4C4, H4/B, H4FB, HIST1H4D, H4C5, H4/J, H4FJ, HIST1H4E, H4C6, H4/C, H4FC, HIST1H4F, H4C8, H4/H, H4FH, HIST1H4H, H4C9, H4/M, H4FM, HIST1H4I, H4C11, H4/E, H4FE, HIST1H4J, H4C12, H4/D, H4FD, HIST1H4K, H4C13, H4/K, H4FK, HIST1H4L, H4C14, H4/N, H4F2, H4FN, HIST2H4, HIST2H4A, H4C15, H4/O, H4FO, HIST2H4B, H4-16, HIST4H4
UniProt & NIH Common Fund Data Resources
Find proteins for P62805 (Homo sapiens) Explore P62805  Go to UniProtKB:  P62805
PHAROS:  P62805

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2A type 1-B/E	D [auth C], G	133	Homo sapiens	Mutation(s): 0  Gene Names: H2AC4, H2AFM, HIST1H2AB, H2AC8, H2AFA, HIST1H2AE
UniProt & NIH Common Fund Data Resources
Find proteins for P04908 (Homo sapiens) Explore P04908  Go to UniProtKB:  P04908
PHAROS:  P04908

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2B type 1-J	E [auth D], K [auth H]	129	Homo sapiens	Mutation(s): 0  Gene Names: H2BC11, H2BFR, HIST1H2BJ
UniProt & NIH Common Fund Data Resources
Find proteins for P06899 (Homo sapiens) Explore P06899  Go to UniProtKB:  P06899
PHAROS:  P06899

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Isoform 2 of N-lysine methyltransferase KMT5A	J [auth K]	352	Homo sapiens	Mutation(s): 0  Gene Names: KMT5A, PRSET7, SET07, SET8, SETD8 EC: 2.1.1 (PDB Primary Data), 2.1.1.361 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NQR1 (Homo sapiens) Explore Q9NQR1  Go to UniProtKB:  Q9NQR1
PHAROS:  Q9NQR1

Entity ID: 5
Molecule	Chains	Length	Organism	Image
DNA (145-MER)	H [auth I]	145	synthetic construct

Entity ID: 6
Molecule	Chains	Length	Organism	Image
DNA (145-MER)	I [auth J]	145	synthetic construct

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.00 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION	3.1
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-02-10 
Deposition Author(s): Ho, C.-H., Takizawa, Y., Kobayashi, W., Arimura, Y., Kurumizaka, H.

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Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	JP17H01408
Japan Society for the Promotion of Science (JSPS)	Japan	JP18H05534
Japan Society for the Promotion of Science (JSPS)	Japan	JP19K06522
Japan Science and Technology	Japan	JPMJCR16G1
Japan Agency for Medical Research and Development (AMED)	Japan	JP19am0101076
Japan Science and Technology	Japan	JPMJER1901

Revision History  

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