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- EMDB-15278: Human FACT-nucleosome complex in unfolded state -

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Basic information

Entry
Database: EMDB / ID: EMD-15278
TitleHuman FACT-nucleosome complex in unfolded state
Map data
Sample
  • Complex: Human multifunctional histone chaperone FACT complex with nucleosome in unfolded state in presence of curaxin CBL0137
    • Organelle or cellular component: Nucleosome
Biological speciesHomo sapiens (human) / Gallus gallus (chicken)
Methodsingle particle reconstruction / negative staining / Resolution: 37.0 Å
AuthorsVolokh O / Sokolova OS / Studitsky V
Funding support United States, Russian Federation, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)R01 GM119398 United States
Russian Science Foundation19-74-30003 Russian Federation
Russian Foundation for Basic Research20-54-04004 Russian Federation
CitationJournal: Front Mol Biosci / Year: 2022
Title: Mechanism of curaxin-dependent nucleosome unfolding by FACT.
Authors: Olesya I Volokh / Anastasia L Sivkina / Andrey V Moiseenko / Anna V Popinako / Maria G Karlova / Maria E Valieva / Elena Y Kotova / Mikhail P Kirpichnikov / Timothy Formosa / Vasily M ...Authors: Olesya I Volokh / Anastasia L Sivkina / Andrey V Moiseenko / Anna V Popinako / Maria G Karlova / Maria E Valieva / Elena Y Kotova / Mikhail P Kirpichnikov / Timothy Formosa / Vasily M Studitsky / Olga S Sokolova /
Abstract: Human FACT (FACT) is a multifunctional histone chaperone involved in transcription, replication and DNA repair. Curaxins are anticancer compounds that induce FACT-dependent nucleosome unfolding and ...Human FACT (FACT) is a multifunctional histone chaperone involved in transcription, replication and DNA repair. Curaxins are anticancer compounds that induce FACT-dependent nucleosome unfolding and trapping of FACT in the chromatin of cancer cells (c-trapping) through an unknown molecular mechanism. Here, we analyzed the effects of curaxin CBL0137 on nucleosome unfolding by FACT using spFRET and electron microscopy. By itself, FACT adopted multiple conformations, including a novel, compact, four-domain state in which the previously unresolved NTD of the SPT16 subunit of FACT was localized, apparently stabilizing a compact configuration. Multiple, primarily open conformations of FACT-nucleosome complexes were observed during curaxin-supported nucleosome unfolding. The obtained models of intermediates suggest "decision points" in the unfolding/folding pathway where FACT can either promote disassembly or assembly of nucleosomes, with the outcome possibly being influenced by additional factors. The data suggest novel mechanisms of nucleosome unfolding by FACT and c-trapping by curaxins.
History
DepositionJun 28, 2022-
Header (metadata) releaseJul 6, 2022-
Map releaseJul 6, 2022-
UpdateJan 25, 2023-
Current statusJan 25, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_15278.png

Downloads & links

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Map

FileDownload / File: emd_15278.map.gz / Format: CCP4 / Size: 3.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 4.1 Å
Density
Contour LevelBy AUTHOR: 0.0545
Minimum - Maximum-0.035233714 - 0.12405096
Average (Standard dev.)0.00043768258 (±0.009773617)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions100100100
Spacing100100100
CellA=B=C: 410.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_15278_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_15278_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Human multifunctional histone chaperone FACT complex with nucleos...

EntireName: Human multifunctional histone chaperone FACT complex with nucleosome in unfolded state in presence of curaxin CBL0137
Components
  • Complex: Human multifunctional histone chaperone FACT complex with nucleosome in unfolded state in presence of curaxin CBL0137
    • Organelle or cellular component: Nucleosome

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Supramolecule #1: Human multifunctional histone chaperone FACT complex with nucleos...

SupramoleculeName: Human multifunctional histone chaperone FACT complex with nucleosome in unfolded state in presence of curaxin CBL0137
type: complex / ID: 1 / Chimera: Yes / Parent: 0
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #2: Nucleosome

SupramoleculeName: Nucleosome / type: organelle_or_cellular_component / ID: 2 / Parent: 1
Source (natural)Organism: Gallus gallus (chicken)

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Experimental details

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Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
StainingType: NEGATIVE / Material: uranyl acetate

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Electron microscopy

MicroscopeJEOL 2100
Image recordingFilm or detector model: GATAN ULTRASCAN 1000 (2k x 2k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 4.0 µm / Nominal defocus min: 0.6 µm

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Image processing

Particle selectionNumber selected: 95634
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 37.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 2570
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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