7XI9 | pdb_00007xi9

Cryo-EM structure of human DNMT1 (aa:351-1616) in complex with ubiquitinated H3 and hemimethylated DNA analog (CXXC-ordered form)

• PDB DOI: https://doi.org/10.2210/pdb7XI9/pdb
• NAKB: 7XI9
• EM Map EMD-33200: EMDB EMDataResource

• Classification: TRANSFERASE/DNA
• Organism(s): Homo sapiens, synthetic construct
• Expression System: Baculovirus expression vector pFastBac1-HM
• Mutation(s): No 


• Deposited: 2022-04-12 Released: 2022-11-30 
• Deposition Author(s): Onoda, H., Kikuchi, A., Kori, S., Yoshimi, S., Yamagata, A., Arita, K.
• Funding Organization(s): Ministry of Education, Culture, Sports, Science and Technology (Japan), Japan Society for the Promotion of Science (JSPS)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.52 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental

Literature

Structural basis for activation of DNMT1.

Kikuchi, A., Onoda, H., Yamaguchi, K., Kori, S., Matsuzawa, S., Chiba, Y., Tanimoto, S., Yoshimi, S., Sato, H., Yamagata, A., Shirouzu, M., Adachi, N., Sharif, J., Koseki, H., Nishiyama, A., Nakanishi, M., Defossez, P.A., Arita, K.

(2022) Nat Commun 13: 7130-7130

• PubMed: 36414620 
• DOI: https://doi.org/10.1038/s41467-022-34779-4
• Primary Citation Related Structures: 
  7XI9, 7XIB


• PubMed Abstract: 
  

  DNMT1 is an essential enzyme that maintains genomic DNA methylation, and its function is regulated by mechanisms that are not yet fully understood. Here, we report the cryo-EM structure of human DNMT1 bound to its two natural activators: hemimethylated DNA and ubiquitinated histone H3. We find that a hitherto unstudied linker, between the RFTS and CXXC domains, plays a key role for activation. It contains a conserved α-helix which engages a crucial "Toggle" pocket, displacing a previously described inhibitory linker, and allowing the DNA Recognition Helix to spring into the active conformation. This is accompanied by large-scale reorganization of the inhibitory RFTS and CXXC domains, allowing the enzyme to gain full activity. Our results therefore provide a mechanistic basis for the activation of DNMT1, with consequences for basic research and drug design.

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Organizational Affiliation: 
• Structural Biology Laboratory, Graduate School of Medical Life Science, Yokohama City University, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan.
Synchrotron Radiation Research Center, Nagoya University, Furo-Cho, Chikusa-Ku, Nagoya, 464-8603, Japan.
Université Paris Cité, CNRS, Epigenetics and Cell Fate, F-75013, Paris, France.
Division of Cancer Cell Biology, Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan.
Laboratory for Protein Functional and Structural Biology, RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan.
Structural Biology Research Center, Photon Factory, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), 1-1 Oho, Tsukuba, Ibaraki, 305-0801, Japan.
Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences (IMS), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan.
Department of Cellular and Molecular Medicine, Graduate School of Medical and Pharmaceutical Sciences, Chiba University, Chiba, 260-8670, Japan.
Structural Biology Laboratory, Graduate School of Medical Life Science, Yokohama City University, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 151.16 kDa 
• Atom Count: 7,620 
• Modeled Residue Count: 893 
• Deposited Residue Count: 1,290 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA (cytosine-5)-methyltransferase 1	A	1,266	Homo sapiens	Mutation(s): 0  Gene Names: DNMT1 EC: 2.1.1.37
UniProt & NIH Common Fund Data Resources
Find proteins for P26358 (Homo sapiens) Explore P26358  Go to UniProtKB:  P26358
PHAROS:  P26358 GTEx:  ENSG00000130816

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*AP*CP*TP*TP*AP*(5CM)P*GP*GP*AP*AP*GP*G)-3')	B	12	synthetic construct

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*CP*CP*TP*TP*CP*(C55)P*GP*TP*AP*AP*GP*T)-3')	C	12	synthetic construct

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SAH	H [auth A]	S-ADENOSYL-L-HOMOCYSTEINE C14 H20 N6 O5 S ZJUKTBDSGOFHSH-WFMPWKQPSA-N
ZN	D [auth A], E [auth A], F [auth A], G [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.52 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.17.1
RECONSTRUCTION	cryoSPARC	3.2.0

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-11-30 
Deposition Author(s): Onoda, H., Kikuchi, A., Kori, S., Yoshimi, S., Yamagata, A., Arita, K.

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Funding Organization	Location	Grant Number
Ministry of Education, Culture, Sports, Science and Technology (Japan)	Japan	JP18H02392
Ministry of Education, Culture, Sports, Science and Technology (Japan)	Japan	JP19H05294
Ministry of Education, Culture, Sports, Science and Technology (Japan)	Japan	JP19H05741
Japan Society for the Promotion of Science (JSPS)	Japan	SK201904

Revision History  

• Version 1.0: 2022-11-30
  Type: Initial release
  
• Version 1.1: 2022-12-07
  Changes: Database references
• Version 1.2: 2024-07-03
  Changes: Data collection, Refinement description