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- EMDB-63676: UHRF1 bound to a mononucleosome in its pre-active state, with the... -

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Basic information

Entry
Database: EMDB / ID: EMD-63676
TitleUHRF1 bound to a mononucleosome in its pre-active state, with the RING domain bound to the SRA domain.
Map datahUHRF1 bound to a mononucleosome in its pre-active state, with the RING domain bound to the SRA domain (Frame 1).
Sample
  • Complex: Human UHRF1 bound to a mononucleosome.
    • Protein or peptide: Histone H4
    • Protein or peptide: Histone H2A
    • Protein or peptide: Histone H2B 1.1
    • Protein or peptide: Histone H3
    • DNA: DNA (144-MER)
  • Protein or peptide: E3 ubiquitin-protein ligase UHRF1
  • DNA: DNA (144-MER)
  • Ligand: ZINC ION
KeywordsEpigenetic reader/writer protein involved in DNA methylation. / DNA BINDING PROTEIN
Function / homology
Function and homology information


histone H3 ubiquitin ligase activity / DNA damage sensor activity / hemi-methylated DNA-binding / homologous recombination / regulation of epithelial cell proliferation / methyl-CpG binding / histone H3K9me2/3 reader activity / : / negative regulation of gene expression via chromosomal CpG island methylation / positive regulation of protein metabolic process ...histone H3 ubiquitin ligase activity / DNA damage sensor activity / hemi-methylated DNA-binding / homologous recombination / regulation of epithelial cell proliferation / methyl-CpG binding / histone H3K9me2/3 reader activity / : / negative regulation of gene expression via chromosomal CpG island methylation / positive regulation of protein metabolic process / mitotic spindle assembly / protein autoubiquitination / cis-regulatory region sequence-specific DNA binding / heterochromatin / epigenetic regulation of gene expression / replication fork / DNA methylation / Chromatin modifications during the maternal to zygotic transition (MZT) / euchromatin / double-strand break repair via homologous recombination / RING-type E3 ubiquitin transferase / spindle / nuclear matrix / ubiquitin-protein transferase activity / structural constituent of chromatin / ubiquitin protein ligase activity / heterochromatin formation / nucleosome / nucleosome assembly / histone binding / ubiquitin-dependent protein catabolic process / nucleic acid binding / protein ubiquitination / protein heterodimerization activity / DNA damage response / chromatin / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleoplasm / identical protein binding / nucleus
Similarity search - Function
: / UHRF1, tandem tudor domain / Tandem tudor domain within UHRF1 / 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. / PUA-like superfamily ...: / UHRF1, tandem tudor domain / Tandem tudor domain within UHRF1 / 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. / PUA-like superfamily / PHD-finger / 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 / 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, FYVE/PHD-type / 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 / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Zinc finger, RING/FYVE/PHD-type / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
Histone H3 / Histone H2B 1.1 / Histone H4 / Histone H2A / E3 ubiquitin-protein ligase UHRF1
Similarity search - Component
Biological speciesHomo sapiens (human) / Xenopus laevis (African clawed frog)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.1 Å
AuthorsNaschberger A / Baradaran R / Sayed A / Fischle W
Funding support Saudi Arabia, 1 items
OrganizationGrant numberCountry
Other government Saudi Arabia
CitationJournal: To Be Published
Title: The cryo-EM structure of human UHRF1 bound to mononucleosomes.
Authors: Naschberger A / Baradaran R / Sayed A / Fischle W
History
DepositionMar 9, 2025-
Header (metadata) releaseMar 11, 2026-
Map releaseMar 11, 2026-
UpdateMar 11, 2026-
Current statusMar 11, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_63676.png

Downloads & links

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Map

FileDownload / File: emd_63676.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationhUHRF1 bound to a mononucleosome in its pre-active state, with the RING domain bound to the SRA domain (Frame 1).
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.73 Å/pix.
x 384 pix.
= 279.936 Å		0.73 Å/pix.
x 384 pix.
= 279.936 Å		0.73 Å/pix.
x 384 pix.
= 279.936 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.729 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.00126
Minimum - Maximum-0.0047780224 - 0.0099982135
Average (Standard dev.)-0.000046299865 (±0.00031888115)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 279.93597 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_63676_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 1 of hUHRF1 bound to a...

Fileemd_63676_half_map_1.map
AnnotationHalf map 1 of hUHRF1 bound to a mononucleosome in its pre-active state, with the RING domain bound to the SRA domain (Frame 1).
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 2 of hUHRF1 bound to a...

Fileemd_63676_half_map_2.map
AnnotationHalf map 2 of hUHRF1 bound to a mononucleosome in its pre-active state, with the RING domain bound to the SRA domain (Frame 1).
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Human UHRF1 bound to a mononucleosome.

EntireName: Human UHRF1 bound to a mononucleosome.
Components
  • Complex: Human UHRF1 bound to a mononucleosome.
    • Protein or peptide: Histone H4
    • Protein or peptide: Histone H2A
    • Protein or peptide: Histone H2B 1.1
    • Protein or peptide: Histone H3
    • DNA: DNA (144-MER)
  • Protein or peptide: E3 ubiquitin-protein ligase UHRF1
  • DNA: DNA (144-MER)
  • Ligand: ZINC ION

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Supramolecule #1: Human UHRF1 bound to a mononucleosome.

SupramoleculeName: Human UHRF1 bound to a mononucleosome. / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Histone H4

MacromoleculeName: Histone H4 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 11.394426 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MSGRGKGGKG LGKGGAKRHR KVLRDNIQGI TKPAIRRLAR RGGVKRISGL IYEETRGVLK VFLENVIRDA VTYTEHAKRK TVTAMDVVY ALKRQGRTLY GFGG

UniProtKB: Histone H4

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Macromolecule #2: Histone H2A

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

UniProtKB: Histone H2A

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Macromolecule #3: Histone H2B 1.1

MacromoleculeName: Histone H2B 1.1 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 13.965265 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MPEPAKSAPA PKKGSKKAVT KTQKKDGKKR RKSRKESYAI YVYKVLKQVH PDTGISSKAM SIMNSFVNDV FERIAGEASR LAHYNKRST ITSREIQTAV RLLLPGELAK HAVSEGTKAV TKYTSAK

UniProtKB: Histone H2B 1.1

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Macromolecule #4: Histone H3

MacromoleculeName: Histone H3 / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 15.435126 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MARTKQTARK STGGKAPRKQ LATKAARKSA PATGGVKKPH RYRPGTVALR EIRRYQKSTE LLIRKLPFQR LVREIAQDFK TDLRFQSSA VMALQEASEA YLVALFEDTN LCAIHAKRVT IMPKDIQLAR RIRGERA

UniProtKB: Histone H3

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Macromolecule #7: E3 ubiquitin-protein ligase UHRF1

MacromoleculeName: E3 ubiquitin-protein ligase UHRF1 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO / EC number: RING-type E3 ubiquitin transferase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 89.948078 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MWIQVRTMDG RQTHTVDSLS RLTKVEELRR KIQELFHVEP GLQRLFYRGK QMEDGHTLFD YEVRLNDTIQ LLVRQSLVLP HSTKERDSE LSDTDSGCCL GQSESDKSST HGEAAAETDS RPADEDMWDE TELGLYKVNE YVDARDTNMG AWFEAQVVRV T RKAPSRDE ...String:
MWIQVRTMDG RQTHTVDSLS RLTKVEELRR KIQELFHVEP GLQRLFYRGK QMEDGHTLFD YEVRLNDTIQ LLVRQSLVLP HSTKERDSE LSDTDSGCCL GQSESDKSST HGEAAAETDS RPADEDMWDE TELGLYKVNE YVDARDTNMG AWFEAQVVRV T RKAPSRDE PCSSTSRPAL EEDVIYHVKY DDYPENGVVQ MNSRDVRARA RTIIKWQDLE VGQVVMLNYN PDNPKERGFW YD AEISRKR ETRTARELYA NVVLGDDSLN DCRIIFVDEV FKIERPGEGS PMVDNPMRRK SGPSCKHCKD DVNRLCRVCA CHL CGGRQD PDKQLMCDEC DMAFHIYCLD PPLSSVPSED EWYCPECRND ASEVVLAGER LRESKKKAKM ASATSSSQRD WGKG MACVG RTKECTIVPS NHYGPIPGIP VGTMWRFRVQ VSESGVHRPH VAGIHGRSND GAYSLVLAGG YEDDVDHGNF FTYTG SGGR DLSGNKRTAE QSCDQKLTNT NRALALNCFA PINDQEGAEA KDWRSGKPVR VVRNVKGGKN SKYAPAEGNR YDGIYK VVK YWPEKGKSGF LVWRYLLRRD DDEPGPWTKE GKDRIKKLGL TMQYPEGYLE ALANREREKE NSKREEEEQQ EGGFASP RT GKGKWKRKSA GGGPSRAGSP RRTSKKTKVE PYSLTAQQSS LIREDKSNAK LWNEVLASLK DRPASGSPFQ LFLSKVEE T FQCICCQELV FRPITTVCQH NVCKDCLDRS FRAQVFSCPA CRYDLGRSYA MQVNQPLQTV LNQLFPGYGN GR

UniProtKB: E3 ubiquitin-protein ligase UHRF1

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Macromolecule #5: DNA (144-MER)

MacromoleculeName: DNA (144-MER) / type: dna / ID: 5 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 44.262211 KDa
SequenceString: (DG)(DG)(DA)(DG)(DA)(DA)(DT)(DC)(DC)(5CM) (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)(DC) (DA)(DA)(DG)(DC)(DT)(DC)(DT) ...String:
(DG)(DG)(DA)(DG)(DA)(DA)(DT)(DC)(DC)(5CM) (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)(DC) (DA)(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)

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Macromolecule #6: DNA (144-MER)

MacromoleculeName: DNA (144-MER) / type: dna / ID: 6 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 44.648426 KDa
SequenceString: (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) ...String:
(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)(DT) (DG)(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)(DT)(DC) (DC)

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Macromolecule #8: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 8 / Number of copies: 5 / 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: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 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: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 48320
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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