11OA | pdb_000011oa

Cryo-EM structure of human DNMT3A R882H octadecamer

PDB DOI: https://doi.org/10.2210/pdb11OA/pdb
EM Map EMD-75877: EMDB EMDataResource

Classification: TRANSFERASE
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2026-03-05 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: 5.04 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

Validation slider image for 11OA

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

Literature

Cryo-EM structure of human DNMT3A R882H octadecamer

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

To be published.

Macromolecule Content

Total Structure Weight: 1,309.92 kDa
Atom Count: 57,257
Modeled Residue Count: 7,561
Deposited Residue Count: 11,394
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, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R	633	Homo sapiens	Mutation(s): 1 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 AA [auth C] SDF format, chain FB [auth J] SDF format, chain GB [auth L] SDF format, chain HA [auth D] SDF format, chain KB [auth M] SDF format, chain LA [auth E] SDF format, chain LB [auth N] SDF format, chain MA [auth F] SDF format, chain PB [auth O] SDF format, chain QA [auth G] SDF format, chain V [auth A] SDF format, chain WB [auth P] SDF format, chain XA [auth H] SDF format, chain XB [auth Q] SDF format, chain YA [auth I] SDF format, chain Z [auth B] MOL2 format, chain AA [auth C] MOL2 format, chain FB [auth J] MOL2 format, chain GB [auth L] MOL2 format, chain HA [auth D] MOL2 format, chain KB [auth M] MOL2 format, chain LA [auth E] MOL2 format, chain LB [auth N] MOL2 format, chain MA [auth F] MOL2 format, chain PB [auth O] MOL2 format, chain QA [auth G] MOL2 format, chain V [auth A] MOL2 format, chain WB [auth P] MOL2 format, chain XA [auth H] MOL2 format, chain XB [auth Q] MOL2 format, chain YA [auth I] MOL2 format, chain Z [auth B] mmCIF format, chain AA [auth C] mmCIF format, chain FB [auth J] mmCIF format, chain GB [auth L] mmCIF format, chain HA [auth D] mmCIF format, chain KB [auth M] mmCIF format, chain LA [auth E] mmCIF format, chain LB [auth N] mmCIF format, chain MA [auth F] mmCIF format, chain PB [auth O] mmCIF format, chain QA [auth G] mmCIF format, chain V [auth A] mmCIF format, chain WB [auth P] mmCIF format, chain XA [auth H] mmCIF format, chain XB [auth Q] mmCIF format, chain YA [auth I] mmCIF format, chain Z [auth B]	AA [auth C] FB [auth J] GB [auth L] HA [auth D] KB [auth M] AA [auth C], FB [auth J], GB [auth L], HA [auth D], KB [auth M], LA [auth E], LB [auth N], MA [auth F], PB [auth O], QA [auth G], V [auth A], WB [auth P], XA [auth H], XB [auth Q], YA [auth I], Z [auth B]	S-ADENOSYL-L-HOMOCYSTEINE C₁₄ H₂₀ N₆ O₅ S ZJUKTBDSGOFHSH-WFMPWKQPSA-N		Interactions Focus chain AA [auth C] Focus chain FB [auth J] Focus chain GB [auth L] Focus chain HA [auth D] Focus chain KB [auth M] Focus chain LA [auth E] Focus chain LB [auth N] Focus chain MA [auth F] Focus chain PB [auth O] Focus chain QA [auth G] Focus chain V [auth A] Focus chain WB [auth P] Focus chain XA [auth H] Focus chain XB [auth Q] Focus chain YA [auth I] Focus chain Z [auth B] Interactions & Density Focus chain AA [auth C] Focus chain FB [auth J] Focus chain GB [auth L] Focus chain HA [auth D] Focus chain KB [auth M] Focus chain LA [auth E] Focus chain LB [auth N] Focus chain MA [auth F] Focus chain PB [auth O] Focus chain QA [auth G] Focus chain V [auth A] Focus chain WB [auth P] Focus chain XA [auth H] Focus chain XB [auth Q] Focus chain YA [auth I] Focus chain Z [auth B]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain AB [auth I] SDF format, chain BA [auth C] SDF format, chain BB [auth I] SDF format, chain CA [auth C] SDF format, chain CB [auth J] SDF format, chain DA [auth C] SDF format, chain DB [auth J] SDF format, chain EA [auth D] SDF format, chain EB [auth J] SDF format, chain FA [auth D] SDF format, chain GA [auth D] SDF format, chain HB [auth M] SDF format, chain IA [auth E] SDF format, chain IB [auth M] SDF format, chain JA [auth E] SDF format, chain JB [auth M] SDF format, chain KA [auth E] SDF format, chain MB [auth N] SDF format, chain NA [auth F] SDF format, chain NB [auth N] SDF format, chain OA [auth F] SDF format, chain OB [auth N] SDF format, chain PA [auth F] SDF format, chain QB [auth O] SDF format, chain RA [auth G] SDF format, chain RB [auth O] SDF format, chain S [auth A] SDF format, chain SA [auth G] SDF format, chain SB [auth O] SDF format, chain T [auth A] SDF format, chain TA [auth G] SDF format, chain TB [auth P] SDF format, chain U [auth A] SDF format, chain UA [auth H] SDF format, chain UB [auth P] SDF format, chain VA [auth H] SDF format, chain VB [auth P] SDF format, chain W [auth B] SDF format, chain WA [auth H] SDF format, chain X [auth B] SDF format, chain Y [auth B] SDF format, chain ZA [auth I] MOL2 format, chain AB [auth I] MOL2 format, chain BA [auth C] MOL2 format, chain BB [auth I] MOL2 format, chain CA [auth C] MOL2 format, chain CB [auth J] MOL2 format, chain DA [auth C] MOL2 format, chain DB [auth J] MOL2 format, chain EA [auth D] MOL2 format, chain EB [auth J] MOL2 format, chain FA [auth D] MOL2 format, chain GA [auth D] MOL2 format, chain HB [auth M] MOL2 format, chain IA [auth E] MOL2 format, chain IB [auth M] MOL2 format, chain JA [auth E] MOL2 format, chain JB [auth M] MOL2 format, chain KA [auth E] MOL2 format, chain MB [auth N] MOL2 format, chain NA [auth F] MOL2 format, chain NB [auth N] MOL2 format, chain OA [auth F] MOL2 format, chain OB [auth N] MOL2 format, chain PA [auth F] MOL2 format, chain QB [auth O] MOL2 format, chain RA [auth G] MOL2 format, chain RB [auth O] MOL2 format, chain S [auth A] MOL2 format, chain SA [auth G] MOL2 format, chain SB [auth O] MOL2 format, chain T [auth A] MOL2 format, chain TA [auth G] MOL2 format, chain TB [auth P] MOL2 format, chain U [auth A] MOL2 format, chain UA [auth H] MOL2 format, chain UB [auth P] MOL2 format, chain VA [auth H] MOL2 format, chain VB [auth P] MOL2 format, chain W [auth B] MOL2 format, chain WA [auth H] MOL2 format, chain X [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain ZA [auth I] mmCIF format, chain AB [auth I] mmCIF format, chain BA [auth C] mmCIF format, chain BB [auth I] mmCIF format, chain CA [auth C] mmCIF format, chain CB [auth J] mmCIF format, chain DA [auth C] mmCIF format, chain DB [auth J] mmCIF format, chain EA [auth D] mmCIF format, chain EB [auth J] mmCIF format, chain FA [auth D] mmCIF format, chain GA [auth D] mmCIF format, chain HB [auth M] mmCIF format, chain IA [auth E] mmCIF format, chain IB [auth M] mmCIF format, chain JA [auth E] mmCIF format, chain JB [auth M] mmCIF format, chain KA [auth E] mmCIF format, chain MB [auth N] mmCIF format, chain NA [auth F] mmCIF format, chain NB [auth N] mmCIF format, chain OA [auth F] mmCIF format, chain OB [auth N] mmCIF format, chain PA [auth F] mmCIF format, chain QB [auth O] mmCIF format, chain RA [auth G] mmCIF format, chain RB [auth O] mmCIF format, chain S [auth A] mmCIF format, chain SA [auth G] mmCIF format, chain SB [auth O] mmCIF format, chain T [auth A] mmCIF format, chain TA [auth G] mmCIF format, chain TB [auth P] mmCIF format, chain U [auth A] mmCIF format, chain UA [auth H] mmCIF format, chain UB [auth P] mmCIF format, chain VA [auth H] mmCIF format, chain VB [auth P] mmCIF format, chain W [auth B] mmCIF format, chain WA [auth H] mmCIF format, chain X [auth B] mmCIF format, chain Y [auth B] mmCIF format, chain ZA [auth I]	AB [auth I] BA [auth C] BB [auth I] CA [auth C] CB [auth J] AB [auth I], BA [auth C], BB [auth I], CA [auth C], CB [auth J], DA [auth C], DB [auth J], EA [auth D], EB [auth J], FA [auth D], GA [auth D], HB [auth M], IA [auth E], IB [auth M], JA [auth E], JB [auth M], KA [auth E], MB [auth N], NA [auth F], NB [auth N], OA [auth F], OB [auth N], PA [auth F], QB [auth O], RA [auth G], RB [auth O], S [auth A], SA [auth G], SB [auth O], T [auth A], TA [auth G], TB [auth P], U [auth A], UA [auth H], UB [auth P], VA [auth H], VB [auth P], W [auth B], WA [auth H], X [auth B], Y [auth B], ZA [auth I]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain AB [auth I] Focus chain BA [auth C] Focus chain BB [auth I] Focus chain CA [auth C] Focus chain CB [auth J] Focus chain DA [auth C] Focus chain DB [auth J] Focus chain EA [auth D] Focus chain EB [auth J] Focus chain FA [auth D] Focus chain GA [auth D] Focus chain HB [auth M] Focus chain IA [auth E] Focus chain IB [auth M] Focus chain JA [auth E] Focus chain JB [auth M] Focus chain KA [auth E] Focus chain MB [auth N] Focus chain NA [auth F] Focus chain NB [auth N] Focus chain OA [auth F] Focus chain OB [auth N] Focus chain PA [auth F] Focus chain QB [auth O] Focus chain RA [auth G] Focus chain RB [auth O] Focus chain S [auth A] Focus chain SA [auth G] Focus chain SB [auth O] Focus chain T [auth A] Focus chain TA [auth G] Focus chain TB [auth P] Focus chain U [auth A] Focus chain UA [auth H] Focus chain UB [auth P] Focus chain VA [auth H] Focus chain VB [auth P] Focus chain W [auth B] Focus chain WA [auth H] Focus chain X [auth B] Focus chain Y [auth B] Focus chain ZA [auth I] Interactions & Density Focus chain AB [auth I] Focus chain BA [auth C] Focus chain BB [auth I] Focus chain CA [auth C] Focus chain CB [auth J] Focus chain DA [auth C] Focus chain DB [auth J] Focus chain EA [auth D] Focus chain EB [auth J] Focus chain FA [auth D] Focus chain GA [auth D] Focus chain HB [auth M] Focus chain IA [auth E] Focus chain IB [auth M] Focus chain JA [auth E] Focus chain JB [auth M] Focus chain KA [auth E] Focus chain MB [auth N] Focus chain NA [auth F] Focus chain NB [auth N] Focus chain OA [auth F] Focus chain OB [auth N] Focus chain PA [auth F] Focus chain QB [auth O] Focus chain RA [auth G] Focus chain RB [auth O] Focus chain S [auth A] Focus chain SA [auth G] Focus chain SB [auth O] Focus chain T [auth A] Focus chain TA [auth G] Focus chain TB [auth P] Focus chain U [auth A] Focus chain UA [auth H] Focus chain UB [auth P] Focus chain VA [auth H] Focus chain VB [auth P] Focus chain W [auth B] Focus chain WA [auth H] Focus chain X [auth B] Focus chain Y [auth B] Focus chain ZA [auth I]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 5.04 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.21.2_5419
RECONSTRUCTION	cryoSPARC	4.7.1

Structure Validation

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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.