ISDA: 12OG

Deposition Date 2026-04-13

Release Date 2026-10-07

Last Version Date 2026-10-07

Entry Detail

PDB ID:

12OG

Keywords:

Structural protein, LIGASE/DNA

Title:

Cryo-EM structure of Arabidopsis VIM1 in complex with hemi-methylated CG-containing nucleosome 2

Biological Source:

Source Organism(s):

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

Expression System(s):

Escherichia coli bl21(de3)

Method Details:

Experimental Method:

ELECTRON MICROSCOPY

Resolution:

3.60 Å

Aggregation State:

PARTICLE

Reconstruction Method:

SINGLE PARTICLE

Download Validation Report

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:I (auth: A)
Chain Length:515
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:A (auth: B), B (auth: 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:C (auth: D), D (auth: 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:E (auth: F), F (auth: 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:G (auth: H), H (auth: 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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