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- EMDB-63670: The focused refinement map of the TTD-PHD domain of UHRF1 bound t... -

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Basic information

Entry
Database: EMDB / ID: EMD-63670
TitleThe focused refinement map of the TTD-PHD domain of UHRF1 bound to a mononucleosome with hemimethylated DNA at superhelical location -6.2.
Map dataTTD-PHD focused-refined map.
Sample
  • Complex: Human UHRF1 bound to a mononucleosome.
    • Complex: histone
    • Complex: UHRF1 and DNA
KeywordsEpigenetic reader/writer protein involved in DNA methylation. / DNA BINDING PROTEIN
Biological speciesXenopus laevis (African clawed frog) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsNaschberger A / Baradaran R
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_63670.png

Downloads & links

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Map

FileDownload / File: emd_63670.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationTTD-PHD focused-refined map.
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: 0.00249
Minimum - Maximum-0.0060726134 - 0.015148693
Average (Standard dev.)-0.000043698998 (±0.0002847587)
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_63670_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: TTD-PHD focused-refined half map 1.

Fileemd_63670_half_map_1.map
AnnotationTTD-PHD focused-refined half map 1.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: TTD-PHD focused-refined half map 2.

Fileemd_63670_half_map_2.map
AnnotationTTD-PHD focused-refined half map 2.
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.
    • Complex: histone
    • Complex: UHRF1 and DNA

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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-#7

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Supramolecule #2: histone

SupramoleculeName: histone / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#4
Source (natural)Organism: Xenopus laevis (African clawed frog)

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Supramolecule #3: UHRF1 and DNA

SupramoleculeName: UHRF1 and DNA / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #5-#7
Source (natural)Organism: Homo sapiens (human)

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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: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 280260
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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