ISDA: 12OF

Deposition Date 2026-04-13

Release Date 2026-10-07

Last Version Date 2026-10-07

Entry Detail

PDB ID:

12OF

Keywords:

Structural protein/DNA

Title:

Cryo-EM structure of Arabidopsis VIM1 in complex with hemi-methylated CG-containing nucleosome 1

Biological Source:

Source Organism(s):

Arabidopsis thaliana (Taxon ID: 3702)
Xenopus laevis (Taxon ID: 8355)
Homo sapiens (Taxon ID: 9606)

Expression System(s):

Escherichia coli bl21(de3)

Method Details:

Experimental Method:

ELECTRON MICROSCOPY

Resolution:

3.80 Å

Aggregation State:

PARTICLE

Reconstruction Method:

SINGLE PARTICLE

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Macromolecular Entities

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:E3 ubiquitin-protein ligase O
Gene (Uniprot):ORTH2
Chain IDs:A
Chain Length:472
Number of Molecules:1
Biological Source:Arabidopsis thaliana

UniProt ID:Q8VYZ0 Pfam ID:PF13920, PF02182, PF13445 EC:2.3.2.27

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Histone H2A
Gene (Uniprot):LOC494591
Chain IDs:B, C
Chain Length:130
Number of Molecules:2
Biological Source:Xenopus laevis

UniProt ID:Q6AZJ8 Pfam ID:PF00125, PF16211

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Histone H2B 1.1
Chain IDs:D, E
Chain Length:123
Number of Molecules:2
Biological Source:Xenopus laevis

UniProt ID:P02281 Pfam ID:PF00125

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Histone H3.2
Chain IDs:F, G
Chain Length:136
Number of Molecules:2
Biological Source:Xenopus laevis

UniProt ID:P84233 Pfam ID:PF00125

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Histone H4
Chain IDs:H, I
Chain Length:103
Number of Molecules:2
Biological Source:Xenopus laevis

UniProt ID:P62798

Polymer Type:polydeoxyribonucleotide
Molecule:DNA
Chain IDs:J (auth: L)
Chain Length:211
Number of Molecules:1
Biological Source:Homo sapiens

Polymer Type:polydeoxyribonucleotide
Molecule:DNA
Chain IDs:K (auth: M)
Chain Length:211
Number of Molecules:1
Biological Source:Homo sapiens

Ligand Molecules

Primary Citation

Cryo-EM structure of Arabidopsis thaliana VIM1 in complex with hemi-methylated CG nucleosome-1

Chen, X, Song, J.Show

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Primary Citation of related structures

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