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- EMDB-46729: Map with best defined NZF RYBP of ncPRC1RYBP bound to singly modi... -

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Basic information

Entry
Database: EMDB / ID: EMD-46729
TitleMap with best defined NZF RYBP of ncPRC1RYBP bound to singly modified H2AK119Ub nucleosome
Map dataOverall map with best defined NZF RYBP of ncPRC1RYBP bound to singly modified H2AK119Ub nucleosome
Sample
  • Complex: ncPRC1RYBP bound to singly modified H2AK119Ub nucleosome
    • Complex: Histones
      • Complex: Histone H3.2
      • Complex: Histone H4
      • Complex: Histone H2A
      • Complex: Histone H2B 1.1
    • Complex: DNA
      • Complex: DNA (153-MER)
      • Complex: DNA (156-MER)
    • Complex: ncPRC1-RYBP
      • Complex: Polycomb complex protein BMI-1
      • Complex: E3 ubiquitin-protein ligase RING2, Ubiquitin-conjugating enzyme E2 D3
      • Complex: RING1 and YY1-binding protein
    • Complex: Ubiquitin
KeywordsDNA complex protein / hydrolase / structural protein / NUCLEAR PROTEIN-DNA complex / GENE REGULATION
Biological speciesHomo sapiens (human) / Xenopus laevis (African clawed frog) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsGodinez-Lopez V / Valencia-Sanchez MI / Armache JP / Armache K-J
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM115882 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)R01CA266978 United States
The Mark Foundation United States
CitationJournal: Nature / Year: 2024
Title: Read-write mechanisms of H2A ubiquitination by Polycomb repressive complex 1.
Authors: Victoria Godínez López / Marco Igor Valencia-Sánchez / Stephen Abini-Agbomson / Jonathan F Thomas / Rachel Lee / Pablo De Ioannes / Brian A Sosa / Jean-Paul Armache / Karim-Jean Armache /
Abstract: Epigenetic inheritance of silent chromatin domains is fundamental to cellular memory during embryogenesis, but it must overcome the dilution of repressive histone modifications during DNA replication. ...Epigenetic inheritance of silent chromatin domains is fundamental to cellular memory during embryogenesis, but it must overcome the dilution of repressive histone modifications during DNA replication. One such modification, histone H2A lysine 119 monoubiquitination (H2AK119Ub), needs to be re-established by the Polycomb repressive complex 1 (PRC1) E3 ligase to restore the silent Polycomb domain. However, the exact mechanism behind this restoration remains unknown. Here, combining cryo-electron microscopy (cryo-EM) and functional approaches, we characterize the read-write mechanism of the non-canonical PRC1-containing RYBP (ncPRC1). This mechanism, which functions as a positive-feedback loop in epigenetic regulation, emphasizes the pivotal role of ncPRC1 in restoring H2AK119Ub. We observe an asymmetrical binding of ncPRC1 to H2AK119Ub nucleosomes, guided in part by the N-terminal zinc-finger domain of RYBP binding to residual H2AK119Ub on nascent chromatin. This recognition positions the RING domains of RING1B and BMI1 on the unmodified nucleosome side, enabling recruitment of the E2 enzyme to ubiquitinate H2AK119 within the same nucleosome (intra-nucleosome read-write) or across nucleosomes (inter-nucleosome read-write). Collectively, our findings provide key structural and mechanistic insights into the dynamic interplay of epigenetic regulation, highlighting the significance of ncPRC1 in H2AK119Ub restoration to sustain repressive chromatin domains.
History
DepositionAug 24, 2024-
Header (metadata) releaseNov 20, 2024-
Map releaseNov 20, 2024-
UpdateJan 15, 2025-
Current statusJan 15, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_46729.png

Downloads & links

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Map

FileDownload / File: emd_46729.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationOverall map with best defined NZF RYBP of ncPRC1RYBP bound to singly modified H2AK119Ub nucleosome
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 256 pix.
= 277.146 Å		1.08 Å/pix.
x 256 pix.
= 277.146 Å		1.08 Å/pix.
x 256 pix.
= 277.146 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0826 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.25
Minimum - Maximum-0.0 - 1.5925896
Average (Standard dev.)0.008426583 (±0.05382202)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 277.1456 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Sharpened map with best defined NZF RYBP of...

Fileemd_46729_additional_1.map
AnnotationSharpened map with best defined NZF RYBP of ncPRC1RYBP bound to singly modified H2AK119Ub nucleosome, Bfactor -74.6
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: DeepEMhancer map (also used for building) with best...

Fileemd_46729_additional_2.map
AnnotationDeepEMhancer map (also used for building) with best defined NZF RYBP of ncPRC1RYBP bound to singly modified H2AK119Ub nucleosome
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A of map with best defined...

Fileemd_46729_half_map_1.map
AnnotationHalf map A of map with best defined NZF RYBP of ncPRC1RYBP bound to singly modified H2AK119Ub nucleosome
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B of map with best defined...

Fileemd_46729_half_map_2.map
AnnotationHalf map B of map with best defined NZF RYBP of ncPRC1RYBP bound to singly modified H2AK119Ub nucleosome
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : ncPRC1RYBP bound to singly modified H2AK119Ub nucleosome

EntireName: ncPRC1RYBP bound to singly modified H2AK119Ub nucleosome
Components
  • Complex: ncPRC1RYBP bound to singly modified H2AK119Ub nucleosome
    • Complex: Histones
      • Complex: Histone H3.2
      • Complex: Histone H4
      • Complex: Histone H2A
      • Complex: Histone H2B 1.1
    • Complex: DNA
      • Complex: DNA (153-MER)
      • Complex: DNA (156-MER)
    • Complex: ncPRC1-RYBP
      • Complex: Polycomb complex protein BMI-1
      • Complex: E3 ubiquitin-protein ligase RING2, Ubiquitin-conjugating enzyme E2 D3
      • Complex: RING1 and YY1-binding protein
    • Complex: Ubiquitin

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Supramolecule #1: ncPRC1RYBP bound to singly modified H2AK119Ub nucleosome

SupramoleculeName: ncPRC1RYBP bound to singly modified H2AK119Ub nucleosome
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#7
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #2: Histones

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

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Supramolecule #3: DNA

SupramoleculeName: DNA / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #5-#6
Source (natural)Organism: synthetic construct (others)

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Supramolecule #4: ncPRC1-RYBP

SupramoleculeName: ncPRC1-RYBP / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #5-#6
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #5: Ubiquitin

SupramoleculeName: Ubiquitin / type: complex / ID: 5 / Parent: 1 / Macromolecule list: #7
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #6: Histone H3.2

SupramoleculeName: Histone H3.2 / type: complex / ID: 6 / Parent: 2 / Macromolecule list: #1
Source (natural)Organism: Xenopus laevis (African clawed frog)

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Supramolecule #7: Histone H4

SupramoleculeName: Histone H4 / type: complex / ID: 7 / Parent: 2 / Macromolecule list: #2
Source (natural)Organism: Xenopus laevis (African clawed frog)

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Supramolecule #8: Histone H2A

SupramoleculeName: Histone H2A / type: complex / ID: 8 / Parent: 2 / Macromolecule list: #3
Source (natural)Organism: Xenopus laevis (African clawed frog)

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Supramolecule #9: Histone H2B 1.1

SupramoleculeName: Histone H2B 1.1 / type: complex / ID: 9 / Parent: 2 / Macromolecule list: #4
Source (natural)Organism: Xenopus laevis (African clawed frog)

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Supramolecule #10: DNA (153-MER)

SupramoleculeName: DNA (153-MER) / type: complex / ID: 10 / Parent: 3 / Macromolecule list: #5
Source (natural)Organism: synthetic construct (others)

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Supramolecule #11: DNA (156-MER)

SupramoleculeName: DNA (156-MER) / type: complex / ID: 11 / Parent: 3
Source (natural)Organism: synthetic construct (others)

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Supramolecule #12: Polycomb complex protein BMI-1

SupramoleculeName: Polycomb complex protein BMI-1 / type: complex / ID: 12 / Parent: 4 / Macromolecule list: #7
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #13: E3 ubiquitin-protein ligase RING2, Ubiquitin-conjugating enzyme E2 D3

SupramoleculeName: E3 ubiquitin-protein ligase RING2, Ubiquitin-conjugating enzyme E2 D3
type: complex / ID: 13 / Parent: 4 / Macromolecule list: #5
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #14: RING1 and YY1-binding protein

SupramoleculeName: RING1 and YY1-binding protein / type: complex / ID: 14 / Parent: 4 / Macromolecule list: #6
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

Concentration0.1 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number real images: 10157 / Average electron dose: 50.7 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 10753652
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. v4.4.1) / Number images used: 94904
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
Final 3D classificationSoftware - Name: cryoSPARC (ver. v4.4.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
ChainDetailsPDB ID
source_name: AlphaFold, initial_model_type: in silico modelMultimer prediction
source_name: PDB, initial_model_type: experimental model

3tu4

source_name: PDB, initial_model_type: experimental model

8h1t

source_name: PDB, initial_model_type: experimental model

8svf

source_name: PDB, initial_model_type: experimental model

4r8p

source_name: PDB, initial_model_type: experimental model

2d9g

source_name: SwissModel, initial_model_type: in silico modelSwissModelTemplate
source_name: PDB, initial_model_type: experimental model

1ubq

RefinementSpace: REAL

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