8XQC | pdb_00008xqc

Cryo-EM structure of human DNMT1 (aa:351-1616) in complex with ubiquitinated PAF15 and hemimethylated DNA analog

• PDB DOI: https://doi.org/10.2210/pdb8XQC/pdb
• EM Map EMD-38573: EMDB EMDataResource
• NAKB: 8XQC

• Classification: TRANSFERASE
• Organism(s): Homo sapiens, synthetic construct
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2024-01-05 Released: 2025-01-15 
• Deposition Author(s): Kikuchi, A., Hayashi, G., Kori, S., Arita, K.
• Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.25 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Activation of DNMT1 by Chemically Synthesized Dual monoubiquitinated PAF15 Protein

Hayashi, G., Takahashi, Y., Kikuchi, A., Kori, S., Arita, K., Murakami, H.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 151.48 kDa 
• Atom Count: 7,233 
• Modeled Residue Count: 866 
• Deposited Residue Count: 1,295 
• 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	1,271	Homo sapiens	Mutation(s): 0  Gene Names: DNMT1, AIM, CXXC9, DNMT 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 (Subject of Investigation/LOI)	D [auth A]	S-ADENOSYL-L-HOMOCYSTEINE C14 H20 N6 O5 S ZJUKTBDSGOFHSH-WFMPWKQPSA-N
ZN (Subject of Investigation/LOI)	E [auth A], F [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.25 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-01-15 
Deposition Author(s): Kikuchi, A., Hayashi, G., Kori, S., Arita, K.

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Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	18H02392, 19H05294, 19H05741,19J22030

Revision History  

• Version 1.0: 2025-01-15
  Type: Initial release
  
• Version 1.1: 2025-06-25
  Changes: Data collection