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- EMDB-36999: Metaphase mononucleosome -

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Basic information

Entry
Database: EMDB / ID: EMD-36999
TitleMetaphase mononucleosome
Map dataMetaphase mononucleosome class 1
Sample
  • Complex: Nucleosome gyre proximal from RPE-1
KeywordsCell / RPE-1 / nucleus / nucleosome / NUCLEAR PROTEIN
Biological speciesHomo sapiens (human)
Methodsubtomogram averaging / cryo EM / Resolution: 34.3 Å
AuthorsChen JK / Cai S / Liu T / Ruan W / Ng CT / Shi J / Surana U / Gan L
Funding support Singapore, 1 items
OrganizationGrant numberCountry
Ministry of Education (MoE, Singapore)MOE2019-T2-1-140 Singapore
CitationJournal: To Be Published
Title: Nanoscale analysis of human G1 and metaphase chromatin in situ
Authors: Chen JK / Liu T / Cai S / Ruan W / Ng CT / Shi J / Surana U / Gan L
History
DepositionAug 2, 2023-
Header (metadata) releaseAug 7, 2024-
Map releaseAug 7, 2024-
UpdateAug 7, 2024-
Current statusAug 7, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_36999.png

Downloads & links

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Map

FileDownload / File: emd_36999.map.gz / Format: CCP4 / Size: 1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMetaphase mononucleosome class 1
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
6.77 Å/pix.
x 64 pix.
= 433.024 Å		6.77 Å/pix.
x 64 pix.
= 433.024 Å		6.77 Å/pix.
x 64 pix.
= 433.024 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 6.766 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.4
Minimum - Maximum-0.6565628 - 0.9056976
Average (Standard dev.)0.001265859 (±0.06572078)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions646464
Spacing646464
CellA=B=C: 433.024 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Metaphase mononucleosome class 2

Fileemd_36999_additional_1.map
AnnotationMetaphase mononucleosome class 2
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Additional map: Metaphase mononucleosome class 3

Fileemd_36999_additional_2.map
AnnotationMetaphase mononucleosome class 3
Projections & Slices
AxesZYX

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Additional map: Metaphase mononucleosome class 4

Fileemd_36999_additional_3.map
AnnotationMetaphase mononucleosome class 4
Projections & Slices
AxesZYX

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Additional map: Metaphase mononucleosome class 5

Fileemd_36999_additional_4.map
AnnotationMetaphase mononucleosome class 5
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Additional map: Metaphase mononucleosome class 6

Fileemd_36999_additional_5.map
AnnotationMetaphase mononucleosome class 6
Projections & Slices
AxesZYX

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Additional map: Metaphase mononucleosome class 7

Fileemd_36999_additional_6.map
AnnotationMetaphase mononucleosome class 7
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Metaphase mononucleosome class 8

Fileemd_36999_additional_7.map
AnnotationMetaphase mononucleosome class 8
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 1

Fileemd_36999_half_map_1.map
AnnotationHalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 2

Fileemd_36999_half_map_2.map
AnnotationHalf 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 gyre proximal from RPE-1

EntireName: Nucleosome gyre proximal from RPE-1
Components
  • Complex: Nucleosome gyre proximal from RPE-1

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Supramolecule #1: Nucleosome gyre proximal from RPE-1

SupramoleculeName: Nucleosome gyre proximal from RPE-1 / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Homo sapiens (human) / 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
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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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) / Resolution.type: BY AUTHOR / Resolution: 34.3 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: RELION (ver. 3.0.8) / Number subtomograms used: 17224
ExtractionNumber tomograms: 4 / Number images used: 145804 / Reference model: Featureless cylinder / Method: Template matching
Final 3D classificationNumber classes: 1 / Software - Name: RELION (ver. 3.0.8)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0.8)

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