8U5H

Cryo-EM structure of human DNMT3A UDR bound to H2AK119ub1-modified nucleosome

• PDB DOI: https://doi.org/10.2210/pdb8U5H/pdb
• EM Map EMD-41922: EMDB EMDataResource
• NAKB: 8U5H

• Classification: STRUCTURAL PROTEIN/TRANSFERASE/DNA
• Organism(s): Homo sapiens, Xenopus laevis
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2023-09-12 Released: 2024-06-12 
• Deposition Author(s): Chen, X., Song, J.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.23 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Cryo-EM structure of human DNMT3A N-terminal domain bound to H2AK119Ub nucleosome

Chen, X., Song, J.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 11-mer - A2B2C2D2E1F1G1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 11-mer - A6B2C1D1E1 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Hetero 8-mer - A2B2C2D2 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Hetero 8-mer - A2B2C2D2 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content

• Total Structure Weight: 251.17 kDa 
• Atom Count: 13,436 
• Modelled Residue Count: 1,217 
• Deposited Residue Count: 1,616 
• Unique protein chains: 6
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA (cytosine-5)-methyltransferase 3A	A, B	98	Homo sapiens	Mutation(s): 0  Gene Names: DNMT3A
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y6K1 (Homo sapiens) Explore Q9Y6K1  Go to UniProtKB:  Q9Y6K1
PHAROS:  Q9Y6K1 GTEx:  ENSG00000119772

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin	D	76	Homo sapiens	Mutation(s): 0  Gene Names: UBC
UniProt & NIH Common Fund Data Resources
Find proteins for P0CG48 (Homo sapiens) Explore P0CG48  Go to UniProtKB:  P0CG48
PHAROS:  P0CG48 GTEx:  ENSG00000150991

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H3.3C	F [auth I], J [auth O]	136	Xenopus laevis	Mutation(s): 0  Gene Names: h3-5
UniProt
Find proteins for P02302 (Xenopus laevis) Explore P02302  Go to UniProtKB:  P02302

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H4	G [auth J], K [auth Q]	103	Xenopus laevis	Mutation(s): 0  Gene Names: LOC121398084
UniProt
Find proteins for A0A8J1LTD2 (Xenopus laevis) Explore A0A8J1LTD2  Go to UniProtKB:  A0A8J1LTD2

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2A	H [auth K], L [auth R]	130	Xenopus laevis	Mutation(s): 1  Gene Names: h2ac14.L
UniProt
Find proteins for Q6AZJ8 (Xenopus laevis) Explore Q6AZJ8  Go to UniProtKB:  Q6AZJ8

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2B 1.1	I [auth M], M [auth S]	123	Xenopus laevis	Mutation(s): 1
UniProt
Find proteins for P02281 (Xenopus laevis) Explore P02281  Go to UniProtKB:  P02281

Entity ID: 2
Molecule	Chains	Length	Organism	Image
nucleosome DNA	C	180	Homo sapiens

Entity ID: 4
Molecule	Chains	Length	Organism	Image
nucleosome DNA	E [auth H]	180	Homo sapiens

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.23 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-06-12 
Deposition Author(s): Chen, X., Song, J.

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

Revision History  

• Version 1.0: 2024-06-12
  Type: Initial release