9E0F | pdb_00009e0f

A focus of DNMT tetramer (1) of the cryo-EM structure of human DNMT3A2-DNMT3B3 complex bound to di-nucleosome

PDB DOI: https://doi.org/10.2210/pdb9E0F/pdb
EM Map EMD-47354: EMDB EMDataResource

Classification: DNA BINDING PROTEIN
Organism(s): Homo sapiens
Expression System: Spodoptera
Mutation(s): No

Deposited: 2024-10-17 Released: 2026-02-18
Deposition Author(s): Xie, X., Zhou, X.E., Worden, E.J., Jones, P.A.
Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.46 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

Validation slider image for 9E0F

This is version 1.0 of the entry. See complete history.

Literature

The structure basis for de novo DNA methylation in chromatin

Xie, X., Liu, M., Zhou, X.E., Worden, E.J., Jones, P.A.

To be published.

Macromolecule Content

Total Structure Weight: 330.59 kDa
Atom Count: 12,187
Modeled Residue Count: 1,510
Deposited Residue Count: 2,924
Unique protein chains: 2

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Isoform 3 of DNA (cytosine-5)-methyltransferase 3B	A [auth V], B [auth Z]	773	Homo sapiens	Mutation(s): 0 Gene Names: DNMT3B EC: 2.1.1.37
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UBC3 (Homo sapiens) Explore Q9UBC3 Go to UniProtKB: Q9UBC3
PHAROS: Q9UBC3 GTEx: ENSG00000088305
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9UBC3
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA (cytosine-5)-methyltransferase 3A	C [auth U], D [auth Y]	689	Homo sapiens	Mutation(s): 0 Gene Names: DNMT3A EC: 2.1.1.37 (PDB Primary Data), 2.1.1 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y6K1 (Homo sapiens) Explore Q9Y6K1 Go to UniProtKB: Q9Y6K1
PHAROS: Q9Y6K1 GTEx: ENSG00000119772
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9Y6K1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SAH Query on SAH Download:Ideal Coordinates CCD File SDF format, chain O [auth Y] SDF format, chain K [auth U] MOL2 format, chain O [auth Y] MOL2 format, chain K [auth U] mmCIF format, chain O [auth Y] mmCIF format, chain K [auth U]	K [auth U], O [auth Y]	S-ADENOSYL-L-HOMOCYSTEINE C₁₄ H₂₀ N₆ O₅ S ZJUKTBDSGOFHSH-WFMPWKQPSA-N		Interactions Focus chain K [auth U] Focus chain O [auth Y] Interactions & Density Focus chain K [auth U] Focus chain O [auth Y]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain N [auth Y] SDF format, chain M [auth Y] SDF format, chain L [auth Y] SDF format, chain J [auth U] SDF format, chain I [auth U] SDF format, chain H [auth U] SDF format, chain G [auth V] SDF format, chain F [auth V] SDF format, chain E [auth V] MOL2 format, chain N [auth Y] MOL2 format, chain M [auth Y] MOL2 format, chain L [auth Y] MOL2 format, chain J [auth U] MOL2 format, chain I [auth U] MOL2 format, chain H [auth U] MOL2 format, chain G [auth V] MOL2 format, chain F [auth V] MOL2 format, chain E [auth V] mmCIF format, chain N [auth Y] mmCIF format, chain M [auth Y] mmCIF format, chain L [auth Y] mmCIF format, chain J [auth U] mmCIF format, chain I [auth U] mmCIF format, chain H [auth U] mmCIF format, chain G [auth V] mmCIF format, chain F [auth V] mmCIF format, chain E [auth V]	E [auth V] F [auth V] G [auth V] H [auth U] I [auth U] E [auth V], F [auth V], G [auth V], H [auth U], I [auth U], J [auth U], L [auth Y], M [auth Y], N [auth Y]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain E [auth V] Focus chain F [auth V] Focus chain G [auth V] Focus chain H [auth U] Focus chain I [auth U] Focus chain J [auth U] Focus chain L [auth Y] Focus chain M [auth Y] Focus chain N [auth Y] Interactions & Density Focus chain E [auth V] Focus chain F [auth V] Focus chain G [auth V] Focus chain H [auth U] Focus chain I [auth U] Focus chain J [auth U] Focus chain L [auth Y] Focus chain M [auth Y] Focus chain N [auth Y]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.46 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.13_2998:

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2026-02-18

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	R35CA209859

Revision History (Full details and data files)

Version 1.0: 2026-02-18
Type: Initial release

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.