ISDA: 9E3D

Deposition Date 2024-10-23

Release Date 2026-02-18

Last Version Date 2026-02-18

Entry Detail

PDB ID:

9E3D

Keywords:

DNA BINDING PROTEIN/DNA

Title:

Cryo-EM structure of DNMT 3A2/3B3 tetramer in complex with a di-nucleosome with K120R mutant H2B

Biological Source:

Source Organism(s):

Homo sapiens (Taxon ID: 9606)

Expression System(s):

Escherichia coli, Spodoptera

Method Details:

Experimental Method:

ELECTRON MICROSCOPY

Resolution:

3.80 Å

Aggregation State:

PARTICLE

Reconstruction Method:

SINGLE PARTICLE

Download Validation Report

Macromolecular Entities

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Histone H3.2
Gene (Uniprot):H3C15, H3C14, H3C13
Chain IDs:A, E, I (auth: M), M (auth: Q)
Chain Length:135
Number of Molecules:4
Biological Source:Homo sapiens

UniProt ID:Q71DI3 Pfam ID:PF00125

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Histone H4
Gene (Uniprot):H4C1, H4C2, H4C3, H4C4, H4C5, H4C6, H4C8, H4C9, H4C11, H4C12, H4C13, H4C14, H4C15, H4C16
Chain IDs:B, F, J (auth: N), N (auth: R)
Chain Length:103
Number of Molecules:4
Biological Source:Homo sapiens

UniProt ID:P62805 Pfam ID:PF15511

Polymer Type:polypeptide(L)
Molecule:Histone H2A
Chain IDs:C, G, K (auth: O), O (auth: S)
Chain Length:129
Number of Molecules:4
Biological Source:Homo sapiens

Polymer Type:polypeptide(L)
Molecule:Histone H2B K120R
Chain IDs:D, H, L (auth: P), P (auth: T)
Chain Length:123
Number of Molecules:4
Biological Source:Homo sapiens

Polymer Type:polydeoxyribonucleotide
Molecule:DNA (320-MER)
Chain IDs:Q (auth: I)
Chain Length:320
Number of Molecules:1
Biological Source:Homo sapiens

Polymer Type:polydeoxyribonucleotide
Molecule:DNA (320-MER)
Chain IDs:R (auth: J)
Chain Length:320
Number of Molecules:1
Biological Source:Homo sapiens

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:DNA (cytosine-5)-methyltransf
Gene (Uniprot):DNMT3A
Chain IDs:U, V (auth: Y)
Chain Length:689
Number of Molecules:2
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 3 of DNA (cytosine-5)
Gene (Uniprot):DNMT3B
Chain IDs:S (auth: V), T (auth: Z)
Chain Length:773
Number of Molecules:2
Biological Source:Homo sapiens