11OI | pdb_000011oi

Cryo-EM structure of human DNMT3A homo-hexamer

PDB DOI: https://doi.org/10.2210/pdb11OI/pdb
EM Map EMD-75886: 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: 3.66 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

Validation slider image for 11OI

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

Literature

Cryo-EM structure of human DNMT3A homo-hexamer

Song, J., Lu, J., Chen, J.

To be published.

Macromolecule Content

Total Structure Weight: 436.11 kDa
Atom Count: 17,511
Modeled Residue Count: 2,310
Deposited Residue Count: 3,798
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA (cytosine-5)-methyltransferase 3A	A [auth C] B [auth E] C [auth F] D E [auth A] A [auth C], B [auth E], C [auth F], D, E [auth A], F [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
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 S [auth B] SDF format, chain O [auth A] SDF format, chain K [auth D] SDF format, chain G [auth C] MOL2 format, chain S [auth B] MOL2 format, chain O [auth A] MOL2 format, chain K [auth D] MOL2 format, chain G [auth C] mmCIF format, chain S [auth B] mmCIF format, chain O [auth A] mmCIF format, chain K [auth D] mmCIF format, chain G [auth C]	G [auth C], K [auth D], O [auth A], S [auth B]	S-ADENOSYL-L-HOMOCYSTEINE C₁₄ H₂₀ N₆ O₅ S ZJUKTBDSGOFHSH-WFMPWKQPSA-N		Interactions Focus chain G [auth C] Focus chain K [auth D] Focus chain O [auth A] Focus chain S [auth B] Interactions & Density Focus chain G [auth C] Focus chain K [auth D] Focus chain O [auth A] Focus chain S [auth B]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain V [auth B] SDF format, chain U [auth B] SDF format, chain T [auth B] SDF format, chain R [auth A] SDF format, chain Q [auth A] SDF format, chain P [auth A] SDF format, chain N [auth D] SDF format, chain M [auth D] SDF format, chain L [auth D] SDF format, chain J [auth C] SDF format, chain I [auth C] SDF format, chain H [auth C] MOL2 format, chain V [auth B] MOL2 format, chain U [auth B] MOL2 format, chain T [auth B] MOL2 format, chain R [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain P [auth A] MOL2 format, chain N [auth D] MOL2 format, chain M [auth D] MOL2 format, chain L [auth D] MOL2 format, chain J [auth C] MOL2 format, chain I [auth C] MOL2 format, chain H [auth C] mmCIF format, chain V [auth B] mmCIF format, chain U [auth B] mmCIF format, chain T [auth B] mmCIF format, chain R [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain P [auth A] mmCIF format, chain N [auth D] mmCIF format, chain M [auth D] mmCIF format, chain L [auth D] mmCIF format, chain J [auth C] mmCIF format, chain I [auth C] mmCIF format, chain H [auth C]	H [auth C] I [auth C] J [auth C] L [auth D] M [auth D] H [auth C], I [auth C], J [auth C], L [auth D], M [auth D], N [auth D], P [auth A], Q [auth A], R [auth A], T [auth B], U [auth B], V [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain H [auth C] Focus chain I [auth C] Focus chain J [auth C] Focus chain L [auth D] Focus chain M [auth D] Focus chain N [auth D] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Interactions & Density Focus chain H [auth C] Focus chain I [auth C] Focus chain J [auth C] Focus chain L [auth D] Focus chain M [auth D] Focus chain N [auth D] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.66 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.21.2_5419
RECONSTRUCTION	cryoSPARC	3.7.1

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2026-08-19

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	--

Revision History (Full details and data files)

Version 1.0: 2026-08-19
Type: Initial release

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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.