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- EMDB-46731: Composite map of ncPRC1RYBP bound to singly modified H2AK119Ub nu... -

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Basic information

Entry
Database: EMDB / ID: EMD-46731
TitleComposite map of ncPRC1RYBP bound to singly modified H2AK119Ub nucleosome
Map dataComposite map 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: 3.0 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: To Be Published
Title: Structural visualization of read-write mechanisms of histone H2A lysine 119 mono-ubiquitination by Polycomb Repressive Complex 1
Authors: Godinez-Lopez V / Valencia-Sanchez MI / Armache JP / Armache K-J
History
DepositionAug 24, 2024-
Header (metadata) releaseNov 20, 2024-
Map releaseNov 20, 2024-
UpdateNov 20, 2024-
Current statusNov 20, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_46731.png

Downloads & links

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Map

FileDownload / File: emd_46731.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationComposite map of ncPRC1RYBP bound to singly modified H2AK119Ub nucleosome
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (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: 3.9
Minimum - Maximum-7.281368 - 42.509856999999997
Average (Standard dev.)-0.03587107 (±0.93844444)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
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: Overall map ncPRC1RYBP bound to singly modified H2AK119Ub...

Fileemd_46731_additional_1.map
AnnotationOverall map ncPRC1RYBP bound to singly modified H2AK119Ub nucleosome, map 1, resampled on Map 3
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: DeepEMhancer map focused on NZF RYBP of ncPRC1RYBP...

Fileemd_46731_additional_2.map
AnnotationDeepEMhancer map focused on NZF RYBP of ncPRC1RYBP bound to singly modified H2AK119Ub nucleosome, map 2, resampled on map3
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Sharpened map focused on RING1B/BMI1 of ncPRC1RYBP bound...

Fileemd_46731_additional_3.map
AnnotationSharpened map focused on RING1B/BMI1 of ncPRC1RYBP bound to singly modified H2AK119Ub nucleosome,map 3, B-factor -63.7
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-#10
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: #7-#9
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #5: Ubiquitin

SupramoleculeName: Ubiquitin / type: complex / ID: 5 / Parent: 1 / Macromolecule list: #10
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 / Macromolecule list: #6
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: #8
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: #9
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: 3.0 Å / Resolution method: OTHER / Software - Name: cryoSPARC (ver. 4.4) / Number images used: 206339
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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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 / Protocol: OTHER

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