ISDA: 9Y4P

Deposition Date 2025-09-03

Release Date 2026-02-18

Last Version Date 2026-02-18

Entry Detail

PDB ID:

9Y4P

Keywords:

DNA BINDING PROTEIN

Title:

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

Biological Source:

Source Organism(s):

Xenopus laevis (Taxon ID: 8355)
Homo sapiens (Taxon ID: 9606)

Expression System(s):

Escherichia coli, Spodoptera

Method Details:

Experimental Method:

ELECTRON MICROSCOPY

Resolution:

3.84 Å

Aggregation State:

PARTICLE

Reconstruction Method:

SINGLE PARTICLE

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Macromolecular Entities

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Histone H3
Gene (Uniprot):LOC121398065
Chain IDs:A
Chain Length:689
Number of Molecules:1
Biological Source:Xenopus laevis

UniProt ID:A0A310TTQ1 Pfam ID:PF00125

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Histone H4
Chain IDs:B, F, K (auth: X), O (auth: R)
Chain Length:103
Number of Molecules:4
Biological Source:Xenopus laevis

UniProt ID:P62799 Pfam ID:PF15511

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Histone H2A type 1
Chain IDs:C, G, L (auth: Y), P (auth: S)
Chain Length:129
Number of Molecules:4
Biological Source:Xenopus laevis

UniProt ID:P06897 Pfam ID:PF00125, PF16211

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Histone H2B 1.1
Chain IDs:D, H, M (auth: P), Q (auth: T)
Chain Length:689
Number of Molecules:4
Biological Source:Xenopus laevis

UniProt ID:P02281 Pfam ID:PF00125

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Histone H3.2
Chain IDs:E, J (auth: W), N (auth: Q)
Chain Length:135
Number of Molecules:3
Biological Source:Xenopus laevis

UniProt ID:P84233 Pfam ID:PF00125

Polymer Type:polydeoxyribonucleotide
Molecule:DNA (321-MER)
Chain IDs:I
Chain Length:321
Number of Molecules:1
Biological Source:Homo sapiens

Polymer Type:polydeoxyribonucleotide
Molecule:DNA (321-MER)
Chain IDs:R (auth: J)
Chain Length:321
Number of Molecules:1
Biological Source:Homo sapiens

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:DNA (cytosine-5)-methyltransferase 3A
Gene (Uniprot):DNMT3A
Chain IDs:U (auth: a), V (auth: c), Y (auth: f), Z (auth: d)
Chain Length:689
Number of Molecules:4
Biological Source:Homo sapiens

UniProt ID:Q9Y6K1 Pfam ID:PF00855, PF17980, PF21255, PF00145 EC:2.1.1.37

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Isoform 7 of DNA (cytosine-5)-methyltransferase 3B
Gene (Uniprot):DNMT3B
Chain IDs:S (auth: b), T (auth: Z), W (auth: e), X (auth: g)
Chain Length:103
Number of Molecules:4
Biological Source:Homo sapiens