9Y4P | pdb_00009y4p

Cryo-EM structure of DNMT3A2/3B3 in complex with H3K36me2 di-nucleosome with eight base pair linker

PDB DOI: https://doi.org/10.2210/pdb9Y4P/pdb
EM Map EMD-72487: EMDB EMDataResource
NAKB: 9Y4P

Classification: DNA BINDING PROTEIN
Organism(s): Xenopus laevis, Homo sapiens
Expression System: Escherichia coli, Spodoptera
Mutation(s): Yes

Deposited: 2025-09-03 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: 3.84 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 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: 992.28 kDa
Atom Count: 48,876
Modeled Residue Count: 5,090
Deposited Residue Count: 7,678
Unique protein chains: 7
Unique nucleic acid chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H3	A	135	Xenopus laevis	Mutation(s): 0 Gene Names: LOC121398065, LOC108703785, LOC121398067
UniProt
Find proteins for A0A310TTQ1 (Xenopus laevis) Explore A0A310TTQ1 Go to UniProtKB: A0A310TTQ1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A310TTQ1
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Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H4	B, F, K [auth X], O [auth R]	103	Xenopus laevis	Mutation(s): 0
UniProt
Find proteins for P62799 (Xenopus laevis) Explore P62799 Go to UniProtKB: P62799
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P62799
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Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2A type 1	C, G, L [auth Y], P [auth S]	129	Xenopus laevis	Mutation(s): 2
UniProt
Find proteins for P06897 (Xenopus laevis) Explore P06897 Go to UniProtKB: P06897
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P06897
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Reference Sequence

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| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2B 1.1	D, H, M [auth P], Q [auth T]	123	Xenopus laevis	Mutation(s): 1
UniProt
Find proteins for P02281 (Xenopus laevis) Explore P02281 Go to UniProtKB: P02281
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P02281
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Reference Sequence

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| 3D Structure

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H3.2	E, J [auth W], N [auth Q]	135	Xenopus laevis	Mutation(s): 1
UniProt
Find proteins for P84233 (Xenopus laevis) Explore P84233 Go to UniProtKB: P84233
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P84233
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Reference Sequence

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| 3D Structure

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
Isoform 7 of DNA (cytosine-5)-methyltransferase 3B	S [auth b], T [auth Z], W [auth e], X [auth g]	580	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: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA (cytosine-5)-methyltransferase 3A	U [auth a], V [auth c], Y [auth f], Z [auth d]	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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(by identity cutoff)

Molecule	Chains	Length	Organism
Entity ID: 6
DNA (321-MER)	I	321	Homo sapiens
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Reference Sequence

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Molecule	Chains	Length	Organism
Entity ID: 7
DNA (321-MER)	R [auth J]	321	Homo sapiens
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SAH (Subject of Investigation/LOI) Query on SAH Download:Ideal Coordinates CCD File SDF format, chain VA [auth d] SDF format, chain RA [auth f] SDF format, chain KA [auth c] SDF format, chain GA [auth a] MOL2 format, chain VA [auth d] MOL2 format, chain RA [auth f] MOL2 format, chain KA [auth c] MOL2 format, chain GA [auth a] mmCIF format, chain VA [auth d] mmCIF format, chain RA [auth f] mmCIF format, chain KA [auth c] mmCIF format, chain GA [auth a]	GA [auth a], KA [auth c], RA [auth f], VA [auth d]	S-ADENOSYL-L-HOMOCYSTEINE C₁₄ H₂₀ N₆ O₅ S ZJUKTBDSGOFHSH-WFMPWKQPSA-N		Interactions Focus chain GA [auth a] Focus chain KA [auth c] Focus chain RA [auth f] Focus chain VA [auth d] Interactions & Density Focus chain GA [auth a] Focus chain KA [auth c] Focus chain RA [auth f] Focus chain VA [auth d]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain UA [auth d] SDF format, chain TA [auth d] SDF format, chain SA [auth d] SDF format, chain QA [auth f] SDF format, chain PA [auth f] SDF format, chain OA [auth f] SDF format, chain NA [auth e] SDF format, chain MA [auth e] SDF format, chain LA [auth e] SDF format, chain JA [auth c] SDF format, chain IA [auth c] SDF format, chain HA [auth c] SDF format, chain FA [auth a] SDF format, chain EA [auth a] SDF format, chain DA [auth a] SDF format, chain CA [auth b] SDF format, chain BA [auth b] SDF format, chain AA [auth b] MOL2 format, chain UA [auth d] MOL2 format, chain TA [auth d] MOL2 format, chain SA [auth d] MOL2 format, chain QA [auth f] MOL2 format, chain PA [auth f] MOL2 format, chain OA [auth f] MOL2 format, chain NA [auth e] MOL2 format, chain MA [auth e] MOL2 format, chain LA [auth e] MOL2 format, chain JA [auth c] MOL2 format, chain IA [auth c] MOL2 format, chain HA [auth c] MOL2 format, chain FA [auth a] MOL2 format, chain EA [auth a] MOL2 format, chain DA [auth a] MOL2 format, chain CA [auth b] MOL2 format, chain BA [auth b] MOL2 format, chain AA [auth b] mmCIF format, chain UA [auth d] mmCIF format, chain TA [auth d] mmCIF format, chain SA [auth d] mmCIF format, chain QA [auth f] mmCIF format, chain PA [auth f] mmCIF format, chain OA [auth f] mmCIF format, chain NA [auth e] mmCIF format, chain MA [auth e] mmCIF format, chain LA [auth e] mmCIF format, chain JA [auth c] mmCIF format, chain IA [auth c] mmCIF format, chain HA [auth c] mmCIF format, chain FA [auth a] mmCIF format, chain EA [auth a] mmCIF format, chain DA [auth a] mmCIF format, chain CA [auth b] mmCIF format, chain BA [auth b] mmCIF format, chain AA [auth b]	AA [auth b] BA [auth b] CA [auth b] DA [auth a] EA [auth a] AA [auth b], BA [auth b], CA [auth b], DA [auth a], EA [auth a], FA [auth a], HA [auth c], IA [auth c], JA [auth c], LA [auth e], MA [auth e], NA [auth e], OA [auth f], PA [auth f], QA [auth f], SA [auth d], TA [auth d], UA [auth d]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain AA [auth b] Focus chain BA [auth b] Focus chain CA [auth b] Focus chain DA [auth a] Focus chain EA [auth a] Focus chain FA [auth a] Focus chain HA [auth c] Focus chain IA [auth c] Focus chain JA [auth c] Focus chain LA [auth e] Focus chain MA [auth e] Focus chain NA [auth e] Focus chain OA [auth f] Focus chain PA [auth f] Focus chain QA [auth f] Focus chain SA [auth d] Focus chain TA [auth d] Focus chain UA [auth d] Interactions & Density Focus chain AA [auth b] Focus chain BA [auth b] Focus chain CA [auth b] Focus chain DA [auth a] Focus chain EA [auth a] Focus chain FA [auth a] Focus chain HA [auth c] Focus chain IA [auth c] Focus chain JA [auth c] Focus chain LA [auth e] Focus chain MA [auth e] Focus chain NA [auth e] Focus chain OA [auth f] Focus chain PA [auth f] Focus chain QA [auth f] Focus chain SA [auth d] Focus chain TA [auth d] Focus chain UA [auth d]