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- EMDB-31086: Subtomogram average of a yeast nucleosome from BY4741 cells -

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Basic information

Entry
Database: EMDB / ID: EMD-31086
TitleSubtomogram average of a yeast nucleosome from BY4741 cells
Map dataClass 1
Sample
  • Complex: Nucleosome from budding yeast BY4741
KeywordsCell / yeast / nucleus / nucleosome / H2A / NUCLEAR PROTEIN / GFP
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsubtomogram averaging / cryo EM / Resolution: 24.0 Å
AuthorsTan ZY / Cai S / Noble AJ / Chen JK / Shi J / Gan L
Funding support Singapore, United States, 9 items
OrganizationGrant numberCountry
Ministry of Education (MoE, Singapore)R-154-000-A49-114 Singapore
Ministry of Education (MoE, Singapore)MOE2019-T2-1-140 Singapore
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)F32GM128303 United States
Simons FoundationSF349247 United States
Other governmentNYSTAR
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM103310 United States
Other privateAgouron Institute F00316
National Institutes of Health/Office of the DirectorOD019994 United States
National Institutes of Health/National Center for Research Resources (NIH/NCRR)RR029300 United States
CitationJournal: Elife / Year: 2023
Title: Heterogeneous non-canonical nucleosomespredominate in yeast cells in situ
Authors: Tan ZY / Cai S / Noble AJ / Chen JK / Shi J / Gan L
History
DepositionMar 22, 2021-
Header (metadata) releaseApr 6, 2022-
Map releaseApr 6, 2022-
UpdateJun 21, 2023-
Current statusJun 21, 2023Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_31086.png

Downloads & links

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Map

FileDownload / File: emd_31086.map.gz / Format: CCP4 / Size: 182.6 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationClass 1
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
6.8 Å/pix.
x 36 pix.
= 244.8 Å		6.8 Å/pix.
x 36 pix.
= 244.8 Å		6.8 Å/pix.
x 36 pix.
= 244.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 6.8 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.5
Minimum - Maximum-0.66002685 - 2.201534
Average (Standard dev.)0.046052508 (±0.20926857)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions363636
Spacing363636
CellA=B=C: 244.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Class 2, half map 1

Fileemd_31086_additional_1.map
AnnotationClass 2, half map 1
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

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Additional map: Class 2

Fileemd_31086_additional_2.map
AnnotationClass 2
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Class 2, half map 2

Fileemd_31086_additional_3.map
AnnotationClass 2, half map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Class 1, half map 1

Fileemd_31086_half_map_1.map
AnnotationClass 1, half map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Class 1, half map 2

Fileemd_31086_half_map_2.map
AnnotationClass 1, 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 : Nucleosome from budding yeast BY4741

EntireName: Nucleosome from budding yeast BY4741
Components
  • Complex: Nucleosome from budding yeast BY4741

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Supramolecule #1: Nucleosome from budding yeast BY4741

SupramoleculeName: Nucleosome from budding yeast BY4741 / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: BY4741 / Organelle: Nucleus

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statecell

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Sample preparation

BufferpH: 7
GridModel: C-flat / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: blot time: 1 second, blot force: 1.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsPhase plate: VOLTA PHASE PLATE / Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Detector mode: INTEGRATING / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number grids imaged: 1 / Average electron dose: 2.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 30369 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 0.1 µm / Nominal defocus min: 0.1 µm / Nominal magnification: 18000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 24.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: RELION (ver. 3.0.8) / Number subtomograms used: 453
ExtractionNumber tomograms: 5 / Number images used: 129473 / Reference model: Featureless cylinder / Method: Template matching / Software - Name: PEET (ver. 1.15)
Final 3D classificationNumber classes: 2 / Software - Name: RELION (ver. 3.0.8)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0.8)

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