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- PDB-12of: Cryo-EM structure of Arabidopsis VIM1 in complex with hemi-methyl... -

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Basic information

Entry
Database: PDB / ID: 12of
TitleCryo-EM structure of Arabidopsis VIM1 in complex with hemi-methylated CG-containing nucleosome 1
Components
  • (DNA) x 2
  • E3 ubiquitin-protein ligase ORTHRUS 2
  • Histone H2A
  • Histone H2B 1.1
  • Histone H3.2
  • Histone H4
KeywordsStructural protein/DNA / E3 ubiquitin ligase / Structural protein-DNA complex
Function / homology
Function and homology information


methyl-CpNpG binding / methyl-CpNpN binding / pericentric heterochromatin formation / double-stranded methylated DNA binding / chromocenter / methyl-CpG binding / negative regulation of gene expression via chromosomal CpG island methylation / RING-type E3 ubiquitin transferase / nucleosomal DNA binding / innate immune response in mucosa ...methyl-CpNpG binding / methyl-CpNpN binding / pericentric heterochromatin formation / double-stranded methylated DNA binding / chromocenter / methyl-CpG binding / negative regulation of gene expression via chromosomal CpG island methylation / RING-type E3 ubiquitin transferase / nucleosomal DNA binding / innate immune response in mucosa / ubiquitin-protein transferase activity / structural constituent of chromatin / nucleosome / histone binding / cell division / chromatin organization / antimicrobial humoral immune response mediated by antimicrobial peptide / heterochromatin formation / antibacterial humoral response / protein ubiquitination / protein heterodimerization activity / chromatin binding / metal ion binding / DNA binding / nucleoplasm / nucleus
Similarity search - Function
: / : / Zinc finger, RING-type, eukaryotic / RING-type zinc-finger / UHRF1/2-like / SRA-YDG / SRA-YDG superfamily / SAD/SRA domain / YDG domain profile. / SET and RING finger associated domain. Domain of unknown function in SET domain containing proteins and in Deinococcus radiodurans DRA1533. ...: / : / Zinc finger, RING-type, eukaryotic / RING-type zinc-finger / UHRF1/2-like / SRA-YDG / SRA-YDG superfamily / SAD/SRA domain / YDG domain profile. / SET and RING finger associated domain. Domain of unknown function in SET domain containing proteins and in Deinococcus radiodurans DRA1533. / Zinc finger, C3HC4 type (RING finger) / PUA-like superfamily / Zinc finger, PHD-type, conserved site / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Zinc finger PHD-type signature. / Ring finger / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / : / : / Histone H2A conserved site / Histone H2A signature. / Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A, C-terminal domain / C-terminus of histone H2A / Zinc finger, FYVE/PHD-type / Histone 2A / Histone H2A / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / Zinc finger RING-type profile. / Zinc finger, RING-type / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 domain / Histone-fold / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
DNA / DNA (> 10) / DNA (> 100) / Histone H2B 1.1 / Histone H4 / Histone H3.2 / Histone H2A / E3 ubiquitin-protein ligase ORTHRUS 2
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
Xenopus laevis (African clawed frog)
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsChen, X. / Song, J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM119721 United States
CitationJournal: To Be Published
Title: Cryo-EM structure of Arabidopsis thaliana VIM1 in complex with hemi-methylated CG nucleosome-1
Authors: Chen, X. / Song, J.
History
DepositionApr 13, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 7, 2026Provider: repository / Type: Initial release
Revision 1.0Oct 7, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: E3 ubiquitin-protein ligase ORTHRUS 2
B: Histone H2A
C: Histone H2A
D: Histone H2B 1.1
E: Histone H2B 1.1
F: Histone H3.2
G: Histone H3.2
H: Histone H4
I: Histone H4
L: DNA
M: DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)292,70415
Polymers292,44211
Non-polymers2624
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Protein , 5 types, 9 molecules ABCDEFGHI

#1: Protein E3 ubiquitin-protein ligase ORTHRUS 2 / Protein VARIANT IN METHYLATION 1 / RING-type E3 ubiquitin transferase ORTHRUS 2


Mass: 52943.523 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: ORTH2, VIM1, At1g57820, F12K22.14 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q8VYZ0, RING-type E3 ubiquitin transferase
#2: Protein Histone H2A


Mass: 14109.436 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: hist1h2aj, LOC494591, XELAEV_18003602mg / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q6AZJ8
#3: Protein Histone H2B 1.1 / H2B1.1


Mass: 13655.948 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P02281
#4: Protein Histone H3.2 / Histone H3


Mass: 15435.126 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P84233
#5: Protein Histone H4


Mass: 11394.426 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P62798

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DNA chain , 2 types, 2 molecules LM

#6: DNA chain DNA


Mass: 65141.477 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#7: DNA chain DNA


Mass: 65167.492 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Non-polymers , 1 types, 4 molecules

#8: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn

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Details

Has ligand of interestN
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1Cryo-EM structure of Arabidopsis thaliana VIM1 in complex with hemi-methylated CG nucleosome-1COMPLEX#2-#70RECOMBINANT
2VIM1COMPLEX1RECOMBINANT
3histoneCOMPLEX1RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Arabidopsis thaliana (thale cress)3702
32Arabidopsis thaliana (thale cress)3702
43Xenopus laevis (African clawed frog)8355
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
21Escherichia coli BL21(DE3) (bacteria)469008
32Escherichia coli BL21(DE3) (bacteria)469008
43Escherichia coli BL21(DE3) (bacteria)469008
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3100 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.8 Å / Resolution method: FSC 0.5 CUT-OFF / Num. of particles: 331378 / Symmetry type: POINT
RefinementHighest resolution: 3.8 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00416972
ELECTRON MICROSCOPYf_angle_d0.67124381
ELECTRON MICROSCOPYf_dihedral_angle_d28.824941
ELECTRON MICROSCOPYf_chiral_restr0.0362746
ELECTRON MICROSCOPYf_plane_restr0.0051956

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