11OH | pdb_000011oh

Cryo-EM structure of human DNMT3A homo-tetramer

PDB DOI: https://doi.org/10.2210/pdb11OH/pdb
EM Map EMD-75885: EMDB EMDataResource

Classification: TRANSFERASE
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2026-03-06 Released: 2026-08-19
Deposition Author(s): Song, J., Lu, J., Chen, J.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.58 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Multidomain interaction governs the filamentous assembly of the dominant-negative DNMT3A R882H mutant.

Chen, J., Lu, J., Long, Z., Yoon, S., Fukunaga, M., Song, J.

(2026) Proc Natl Acad Sci U S A 123: e2609226123-e2609226123

PubMed: 42640801 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1073/pnas.2609226123
Primary Citation Related Structures:
11NZ, 11OA, 11OH, 11OI

PubMed Abstract:
DNA methyltransferase DNMT3A-mediated de novo DNA methylation is important for proper regulation of gene expression and genomic stability in development. The DNMT3A R882H (DNMT3A ^R882H) mutation, a hot-spot mutation in acute myeloid leukemia and developmental disorders, exerts a dominant-negative effect in DNMT3A-mediated DNA methylation through promoting high-order protein assembly. However, due to the lack of structural knowledge on DNMT3A homo-oligomers, the mechanism behind wild-type DNMT3A (DNMT3A ^WT) and DNMT3A ^R882H polymerization remains unclear. Here, we report the single-particle cryo-EM structures of homo-oligomeric DNMT3A ^WT and filamentous DNMT3A ^R882H, revealing the role of the regulatory Pro-Trp-Trp-Pro (PWWP) and ATRX-DNMT3-DNMT3L (ADD) domains of DNMT3A in their dynamic assembly. While the oligomeric assembly of DNMT3A is mainly driven by the well-characterized oligomer interfaces in the methyltransferase domain, the autoinhibitory interaction of the PWWP and ADD domains in DNMT3A places them in a position for intermolecular contact, thereby contributing to the filamentous assembly of DNMT3A ^R882H. Disrupting the autoinhibitory interaction facilitates the transition of DNMT3A ^R882H polymer toward the low-order oligomeric assembly, reinforcing the aggregation-attenuation effect of the previously characterized oligomer-interface mutation R676K. Together, this study uncovers a multidomain cooperated assembly mechanism for DNMT3A, with important implication in development of effective therapeutic strategies against DNMT3A ^R882H-associated diseases.

Organizational Affiliation

Department of Biochemistry, University of California, Riverside, CA 92521.

Macromolecule Content

Total Structure Weight: 290.93 kDa
Atom Count: 12,658
Modeled Residue Count: 1,585
Deposited Residue Count: 2,532
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA (cytosine-5)-methyltransferase 3A	A, B [auth C], C [auth D], D [auth B]	633	Homo sapiens	Mutation(s): 0 Gene Names: DNMT3A EC: 2.1.1.37 (PDB Primary Data), 2.1.1 (PDB Primary Data)
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 M [auth B] SDF format, chain I [auth D] SDF format, chain E [auth C] MOL2 format, chain M [auth B] MOL2 format, chain I [auth D] MOL2 format, chain E [auth C] mmCIF format, chain M [auth B] mmCIF format, chain I [auth D] mmCIF format, chain E [auth C]	E [auth C], I [auth D], M [auth B]	S-ADENOSYL-L-HOMOCYSTEINE C₁₄ H₂₀ N₆ O₅ S ZJUKTBDSGOFHSH-WFMPWKQPSA-N		Interactions Focus chain E [auth C] Focus chain I [auth D] Focus chain M [auth B] Interactions & Density Focus chain E [auth C] Focus chain I [auth D] Focus chain M [auth B]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain P [auth B] SDF format, chain O [auth B] SDF format, chain N [auth B] SDF format, chain L [auth D] SDF format, chain K [auth D] SDF format, chain J [auth D] SDF format, chain H [auth C] SDF format, chain G [auth C] SDF format, chain F [auth C] MOL2 format, chain P [auth B] MOL2 format, chain O [auth B] MOL2 format, chain N [auth B] MOL2 format, chain L [auth D] MOL2 format, chain K [auth D] MOL2 format, chain J [auth D] MOL2 format, chain H [auth C] MOL2 format, chain G [auth C] MOL2 format, chain F [auth C] mmCIF format, chain P [auth B] mmCIF format, chain O [auth B] mmCIF format, chain N [auth B] mmCIF format, chain L [auth D] mmCIF format, chain K [auth D] mmCIF format, chain J [auth D] mmCIF format, chain H [auth C] mmCIF format, chain G [auth C] mmCIF format, chain F [auth C]	F [auth C] G [auth C] H [auth C] J [auth D] K [auth D] F [auth C], G [auth C], H [auth C], J [auth D], K [auth D], L [auth D], N [auth B], O [auth B], P [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain F [auth C] Focus chain G [auth C] Focus chain H [auth C] Focus chain J [auth D] Focus chain K [auth D] Focus chain L [auth D] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Interactions & Density Focus chain F [auth C] Focus chain G [auth C] Focus chain H [auth C] Focus chain J [auth D] Focus chain K [auth D] Focus chain L [auth D] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B]