9E3U | pdb_00009e3u

Cryo-EM structure of DNMT 3A2/3B3 tetramer bound to a di-nucleosome with a 25 base-pair linker

PDB DOI: https://doi.org/10.2210/pdb9E3U/pdb
EM Map EMD-47496: EMDB EMDataResource
NAKB: 9E3U

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

Deposited: 2024-10-24 Released: 2026-01-21
Deposition Author(s): Xie, X., Zhou, X.E., Worden, E., Jones, P.
Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 4.90 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

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

Literature

The structural basis for de novo DNA methylation in chromatin

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

To be published.

Macromolecule Content

Total Structure Weight: 627.84 kDa
Atom Count: 23,771
Modeled Residue Count: 2,447
Deposited Residue Count: 5,007
Unique protein chains: 6
Unique nucleic acid chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H3.2	A, E	135	Homo sapiens	Mutation(s): 0 Gene Names: H3C15, HIST2H3A, H3C14, H3F2, H3FM, HIST2H3C, H3C13, HIST2H3D
UniProt & NIH Common Fund Data Resources
Find proteins for Q71DI3 (Homo sapiens) Explore Q71DI3 Go to UniProtKB: Q71DI3
PHAROS: Q71DI3 GTEx: ENSG00000183598 ENSG00000203811 ENSG00000203852
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q71DI3
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H4	B, F	103	Homo sapiens	Mutation(s): 0 Gene Names: HIST1H4A, H4/A, H4FA, HIST1H4B, H4/I, H4FI, HIST1H4C, H4/G, H4FG, HIST1H4D... HIST1H4A, H4/A, H4FA, HIST1H4B, H4/I, H4FI, HIST1H4C, H4/G, H4FG, HIST1H4D, H4/B, H4FB, HIST1H4E, H4/J, H4FJ, HIST1H4F, H4/C, H4FC, HIST1H4H, H4/H, H4FH, HIST1H4I, H4/M, H4FM, HIST1H4J, H4/E, H4FE, HIST1H4K, H4/D, H4FD, HIST1H4L, H4/K, H4FK, HIST2H4A, H4/N, H4F2, H4FN, HIST2H4, HIST2H4B, H4/O, H4FO, HIST4H4
UniProt & NIH Common Fund Data Resources
Find proteins for P62805 (Homo sapiens) Explore P62805 Go to UniProtKB: P62805
PHAROS: P62805 GTEx: ENSG00000274618 ENSG00000197238 ENSG00000197837 ENSG00000158406 ENSG00000278705 ENSG00000197061 ENSG00000270882 ENSG00000270276 ENSG00000273542 ENSG00000277157 ENSG00000276966 ENSG00000276180 ENSG00000278637 ENSG00000275126
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P62805
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2A	C, G	129	Homo sapiens	Mutation(s): 0

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| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2B	D, H	123	Homo sapiens	Mutation(s): 0 Gene Names: XENTR_v90029538mg
UniProt
Find proteins for A0A1B8Y854 (Xenopus tropicalis) Explore A0A1B8Y854 Go to UniProtKB: A0A1B8Y854
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A1B8Y854
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Reference Sequence

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| 3D Structure

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Isoform 3 of DNA (cytosine-5)-methyltransferase 3B	I [auth L], L [auth V], M [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
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Reference Sequence

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| 3D Structure

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA (cytosine-5)-methyltransferase 3A	N [auth U], O [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
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Reference Sequence

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Molecule	Chains	Length	Organism
Entity ID: 6
DNA (165-MER)	J [auth I]	165	Homo sapiens
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Reference Sequence

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Molecule	Chains	Length	Organism
Entity ID: 7
DNA (165-MER)	K [auth J]	165	Homo sapiens
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 Z [auth Y] SDF format, chain V [auth U] MOL2 format, chain Z [auth Y] MOL2 format, chain V [auth U] mmCIF format, chain Z [auth Y] mmCIF format, chain V [auth U]	V [auth U], Z [auth Y]	S-ADENOSYL-L-HOMOCYSTEINE C₁₄ H₂₀ N₆ O₅ S ZJUKTBDSGOFHSH-WFMPWKQPSA-N		Interactions Focus chain V [auth U] Focus chain Z [auth Y] Interactions & Density Focus chain V [auth U] Focus chain Z [auth Y]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain P [auth V] SDF format, chain S [auth U] SDF format, chain T [auth U] SDF format, chain U SDF format, chain Y SDF format, chain X [auth Y] SDF format, chain W [auth Y] SDF format, chain R [auth V] SDF format, chain Q [auth V] MOL2 format, chain P [auth V] MOL2 format, chain S [auth U] MOL2 format, chain T [auth U] MOL2 format, chain U MOL2 format, chain Y MOL2 format, chain X [auth Y] MOL2 format, chain W [auth Y] MOL2 format, chain R [auth V] MOL2 format, chain Q [auth V] mmCIF format, chain P [auth V] mmCIF format, chain S [auth U] mmCIF format, chain T [auth U] mmCIF format, chain U mmCIF format, chain Y mmCIF format, chain X [auth Y] mmCIF format, chain W [auth Y] mmCIF format, chain R [auth V] mmCIF format, chain Q [auth V]	P [auth V] Q [auth V] R [auth V] S [auth U] T [auth U] P [auth V], Q [auth V], R [auth V], S [auth U], T [auth U], U, W [auth Y], X [auth Y], Y	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain P [auth V] Focus chain Q [auth V] Focus chain R [auth V] Focus chain S [auth U] Focus chain T [auth U] Focus chain U Focus chain W [auth Y] Focus chain X [auth Y] Focus chain Y Interactions & Density Focus chain P [auth V] Focus chain Q [auth V] Focus chain R [auth V] Focus chain S [auth U] Focus chain T [auth U] Focus chain U Focus chain W [auth Y] Focus chain X [auth Y] Focus chain Y

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 4.90 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2026-01-21

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	R35CA209859
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R35GM147261