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- EMDB-76631: Cryo-EM structure of Arabidopsis VIM1 in complex with hemi-methyl... -

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Basic information

Entry
Database: EMDB / ID: EMD-76631
TitleCryo-EM structure of Arabidopsis VIM1 in complex with hemi-methylated CG-containing nucleosome 2
Map datastructure of Arabidopsis VIM1 in complex with hemi-methylated CG-containing nucleosome 2
Sample
  • Complex: Cryo-EM structure of Arabidopsis thaliana VIM1 in complex with hemi-methylated CG nucleosome-1
    • Complex: VIM1
      • Protein or peptide: E3 ubiquitin-protein ligase ORTHRUS 2
    • Complex: histone
      • Protein or peptide: Histone H2A
      • Protein or peptide: Histone H2B 1.1
      • Protein or peptide: Histone H3.2
      • Protein or peptide: Histone H4
    • DNA: DNA
    • DNA: DNA
  • Ligand: ZINC ION
KeywordsE3 ubiquitin ligase / Structural protein-DNA complex / LIGASE / Structural protein / LIGASE-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
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsChen X / Song J
Funding support United States, 1 items
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, 2026-
Header (metadata) releaseOct 7, 2026-
Map releaseOct 7, 2026-
UpdateOct 7, 2026-
Current statusOct 7, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_76631.png

Downloads & links

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Map

FileDownload / File: emd_76631.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationstructure of Arabidopsis VIM1 in complex with hemi-methylated CG-containing nucleosome 2
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
1.09 Å/pix.
x 384 pix.
= 418.56 Å		1.09 Å/pix.
x 384 pix.
= 418.56 Å		1.09 Å/pix.
x 384 pix.
= 418.56 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.09 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 8.0
Minimum - Maximum-32.838830000000002 - 60.630394000000003
Average (Standard dev.)0.0055854446 (±1.0416023)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 418.56 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Cryo-EM structure of Arabidopsis thaliana VIM1 in complex with he...

EntireName: Cryo-EM structure of Arabidopsis thaliana VIM1 in complex with hemi-methylated CG nucleosome-1
Components
  • Complex: Cryo-EM structure of Arabidopsis thaliana VIM1 in complex with hemi-methylated CG nucleosome-1
    • Complex: VIM1
      • Protein or peptide: E3 ubiquitin-protein ligase ORTHRUS 2
    • Complex: histone
      • Protein or peptide: Histone H2A
      • Protein or peptide: Histone H2B 1.1
      • Protein or peptide: Histone H3.2
      • Protein or peptide: Histone H4
    • DNA: DNA
    • DNA: DNA
  • Ligand: ZINC ION

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Supramolecule #1: Cryo-EM structure of Arabidopsis thaliana VIM1 in complex with he...

SupramoleculeName: Cryo-EM structure of Arabidopsis thaliana VIM1 in complex with hemi-methylated CG nucleosome-1
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4, #6-#7
Source (natural)Organism: Arabidopsis thaliana (thale cress)

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Supramolecule #2: VIM1

SupramoleculeName: VIM1 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #5
Source (natural)Organism: Arabidopsis thaliana (thale cress)

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Supramolecule #3: histone

SupramoleculeName: histone / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #1-#4
Source (natural)Organism: Xenopus laevis (African clawed frog)

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Macromolecule #1: Histone H2A

MacromoleculeName: Histone H2A / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 14.109436 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MSGRGKQGGK TRAKAKTRSS RAGLQFPVGR VHRLLRKGNY AERVGAGAPV YLAAVLEYLT AEILELAGNA ARDNKKTRII PRHLQLAVR NDEELNKLLG RVTIAQGGVL PNIQSVLLPK KTESSKSAKS K

UniProtKB: Histone H2A

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Macromolecule #2: Histone H2B 1.1

MacromoleculeName: Histone H2B 1.1 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 13.655948 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MAKSAPAPKK GSKKAVTKTQ KKDGKKRRKT RKESYAIYVY KVLKQVHPDT GISSKAMSIM NSFVNDVFER IAGEASRLAH YNKRSTITS REIQTAVRLL LPGELAKHAV SEGTKAVTKY TSAK

UniProtKB: Histone H2B 1.1

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Macromolecule #3: Histone H3.2

MacromoleculeName: Histone H3.2 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 15.435126 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MARTKQTARK STGGKAPRKQ LATKAARKSA PATGGVKKPH RYRPGTVALR EIRRYQKSTE LLIRKLPFQR LVREIAQDFK TDLRFQSSA VMALQEASEA YLVALFEDTN LCAIHAKRVT IMPKDIQLAR RIRGERA

UniProtKB: Histone H3.2

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Macromolecule #4: Histone H4

MacromoleculeName: Histone H4 / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 11.394426 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MSGRGKGGKG LGKGGAKRHR KVLRDNIQGI TKPAIRRLAR RGGVKRISGL IYEETRGVLK VFLENVIRDA VTYTEHAKRK TVTAMDVVY ALKRQGRTLY GFGG

UniProtKB: Histone H4

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Macromolecule #5: E3 ubiquitin-protein ligase ORTHRUS 2

MacromoleculeName: E3 ubiquitin-protein ligase ORTHRUS 2 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO / EC number: RING-type E3 ubiquitin transferase
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 57.670445 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: NPNLDVLSAL GDNLMCSFCM QLPERPVTKP CGHNACLKCF EKWMGQGKRT CGKCRSIIPE KMAKNPRINS SLVAAIRLAK VSKSAAATT SKVFHFISNQ DRPDKAFTTE RAKKTGKANA ASGKIYVTIP PDHFGPIPAE NDPVRNQGLL VGESWEDRLE C RQWGAHFP ...String:
NPNLDVLSAL GDNLMCSFCM QLPERPVTKP CGHNACLKCF EKWMGQGKRT CGKCRSIIPE KMAKNPRINS SLVAAIRLAK VSKSAAATT SKVFHFISNQ DRPDKAFTTE RAKKTGKANA ASGKIYVTIP PDHFGPIPAE NDPVRNQGLL VGESWEDRLE C RQWGAHFP HVAGIAGQST YGAQSVALSG GYKDDEDHGE WFLYTGSGGR DLSGNKRTNK EQSFDQKFEK SNAALKLSCK LG YPVRVVR SHKEKRSAYA PEEGVRYDGV YRIEKCWRKV GVQGSFKVCR YLFVRCDNEP APWTSDENGD RPRPIPNIPE LNM ATDLFE RKETPSWDFD EGEGCWKWMK PPPASKKSVN VLAPEERKNL RKAIKAAHSN TMRARLLKEF KCQICQQVLT LPVT TPCAH NFCKACLEAK FAGKTLVRER STGGRTLRSR KNVLNCPCCP TDISDFLQNP QVNREVAEVI EKLKTQEEDT AELED EDEG ECSGTTPEED SEQPKKRIKL DTDATVSATI R

UniProtKB: E3 ubiquitin-protein ligase ORTHRUS 2

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Macromolecule #6: DNA

MacromoleculeName: DNA / type: dna / ID: 6 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 65.192562 KDa
SequenceString: (DT)(DA)(DT)(DG)(DA)(DG)(DT)(DA)(DG)(DT) (DA)(DA)(DT)(DG)(DA)(DC)(DA)(DG)(DA)(DT) (5CM)(DG)(DT)(DA)(DT)(DC)(DA)(DG)(DT) (DG)(DA)(DC)(DA)(DT)(DC)(DC)(DT)(DG)(DT) (DG)(DA)(DA)(DT)(DC)(DC)(DC) ...String:
(DT)(DA)(DT)(DG)(DA)(DG)(DT)(DA)(DG)(DT) (DA)(DA)(DT)(DG)(DA)(DC)(DA)(DG)(DA)(DT) (5CM)(DG)(DT)(DA)(DT)(DC)(DA)(DG)(DT) (DG)(DA)(DC)(DA)(DT)(DC)(DC)(DT)(DG)(DT) (DG)(DA)(DA)(DT)(DC)(DC)(DC)(DG)(DG) (DT)(DG)(DC)(DC)(DG)(DA)(DG)(DG)(DC)(DC) (DG) (DC)(DT)(DC)(DA)(DA)(DT)(DT)(DG) (DG)(DT)(DC)(DG)(DT)(DA)(DG)(DA)(DC)(DA) (DG)(DC) (DT)(DC)(DT)(DA)(DG)(DC)(DA) (DC)(DC)(DG)(DC)(DT)(DT)(DA)(DA)(DA)(DC) (DG)(DC)(DA) (DC)(DG)(DT)(DA)(DC)(DG) (DC)(DG)(DC)(DT)(DG)(DT)(DC)(DC)(DC)(DC) (DC)(DG)(DC)(DG) (DT)(DT)(DT)(DT)(DA) (DA)(DC)(DC)(DG)(DC)(DC)(DA)(DA)(DG)(DG) (DG)(DG)(DA)(DT)(DT) (DA)(DC)(DT)(DC) (DC)(DC)(DT)(DA)(DG)(DT)(DC)(DT)(DC)(DC) (DA)(DG)(DG)(DC)(DA)(DC) (DG)(DT)(DG) (DT)(DC)(DA)(DG)(DA)(DT)(DA)(DT)(DA)(DT) (DA)(DC)(DA)(DT)(DC)(DC)(DT) (DG)(DT) (DT)(DT)(DT)(DT)(DG)(DA)(DT)(DG)(DT)(DG) (DA)(DT)(DG)(DA)(DA)(DT)(DG)(DA) (DA) (DT)(DG)(DG)(DG)(DA)(DA)(DG)(DA)(DG)(DG) (DA)

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Macromolecule #7: DNA

MacromoleculeName: DNA / type: dna / ID: 7 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 65.107523 KDa
SequenceString: (DT)(DC)(DC)(DT)(DC)(DT)(DT)(DC)(DC)(DC) (DA)(DT)(DT)(DC)(DA)(DT)(DT)(DC)(DA)(DT) (DC)(DA)(DC)(DA)(DT)(DC)(DA)(DA)(DA) (DA)(DA)(DC)(DA)(DG)(DG)(DA)(DT)(DG)(DT) (DA) (DT)(DA)(DT)(DA)(DT)(DC) ...String:
(DT)(DC)(DC)(DT)(DC)(DT)(DT)(DC)(DC)(DC) (DA)(DT)(DT)(DC)(DA)(DT)(DT)(DC)(DA)(DT) (DC)(DA)(DC)(DA)(DT)(DC)(DA)(DA)(DA) (DA)(DA)(DC)(DA)(DG)(DG)(DA)(DT)(DG)(DT) (DA) (DT)(DA)(DT)(DA)(DT)(DC)(DT)(DG) (DA)(DC)(DA)(DC)(DG)(DT)(DG)(DC)(DC)(DT) (DG)(DG) (DA)(DG)(DA)(DC)(DT)(DA)(DG) (DG)(DG)(DA)(DG)(DT)(DA)(DA)(DT)(DC)(DC) (DC)(DC)(DT) (DT)(DG)(DG)(DC)(DG)(DG) (DT)(DT)(DA)(DA)(DA)(DA)(DC)(DG)(DC)(DG) (DG)(DG)(DG)(DG) (DA)(DC)(DA)(DG)(DC) (DG)(DC)(DG)(DT)(DA)(DC)(DG)(DT)(DG)(DC) (DG)(DT)(DT)(DT)(DA) (DA)(DG)(DC)(DG) (DG)(DT)(DG)(DC)(DT)(DA)(DG)(DA)(DG)(DC) (DT)(DG)(DT)(DC)(DT)(DA) (DC)(DG)(DA) (DC)(DC)(DA)(DA)(DT)(DT)(DG)(DA)(DG)(DC) (DG)(DG)(DC)(DC)(DT)(DC)(DG) (DG)(DC) (DA)(DC)(DC)(DG)(DG)(DG)(DA)(DT)(DT)(DC) (DA)(DC)(DA)(DG)(DG)(DA)(DT)(DG) (DT) (DC)(DA)(DC)(DT)(DG)(DA)(DT)(DA)(DC)(DG) (DA)(DT)(DC)(DT)(DG)(DT)(DC)(DA)(DT) (DT)(DA)(DC)(DT)(DA)(DC)(DT)(DC)(DA)(DT) (DA)

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Macromolecule #8: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 8 / Number of copies: 3 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.1 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: cryoSPARC / Number images used: 293656
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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