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- EMDB-6949: Subtomogram average of a nucleosome with short linker DNA from a ... -

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Basic information

Entry
Database: EMDB / ID: EMD-6949
TitleSubtomogram average of a nucleosome with short linker DNA from a Volta phase contrast cryotomogram of a cryo-FIB lamella of an interphase HeLa cell
Map dataHeLa nucleosome, short linker
Sample
  • Cell: HeLa cell, interphase
Biological speciesHomo sapiens (human)
Methodsubtomogram averaging / cryo EM / Resolution: 24.0 Å
AuthorsCai S / Bock D / Pilhofer M / Gan L
Funding support Singapore, Switzerland, 4 items
OrganizationGrant numberCountry
Ministry of Education (Singapore)R-154-000-624-112 Singapore
Ministry of Education (Singapore)R-154-000-A49-114 Singapore
Swiss National Science Foundation Switzerland
European Research Council Switzerland
CitationJournal: Mol Biol Cell / Year: 2018
Title: The in situ structures of mono-, di-, and trinucleosomes in human heterochromatin.
Authors: Shujun Cai / Désirée Böck / Martin Pilhofer / Lu Gan /
Abstract: The in situ three-dimensional organization of chromatin at the nucleosome and oligonucleosome levels is unknown. Here we use cryo-electron tomography to determine the in situ structures of HeLa ...The in situ three-dimensional organization of chromatin at the nucleosome and oligonucleosome levels is unknown. Here we use cryo-electron tomography to determine the in situ structures of HeLa nucleosomes, which have canonical core structures and asymmetric, flexible linker DNA. Subtomogram remapping suggests that sequential nucleosomes in heterochromatin follow irregular paths at the oligonucleosome level. This basic principle of higher-order repressive chromatin folding is compatible with the conformational variability of the two linker DNAs at the single-nucleosome level.
History
DepositionApr 28, 2018-
Header (metadata) releaseNov 7, 2018-
Map releaseNov 7, 2018-
UpdateAug 5, 2020-
Current statusAug 5, 2020Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.5
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.5
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_6949.png

Downloads & links

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Map

FileDownload / File: emd_6949.map.gz / Format: CCP4 / Size: 85.9 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHeLa nucleosome, short linker
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
6.9 Å/pix.
x 28 pix.
= 193.2 Å		6.9 Å/pix.
x 28 pix.
= 193.2 Å		6.9 Å/pix.
x 28 pix.
= 193.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 6.9 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.5 / Movie #1: 0.5
Minimum - Maximum-0.757936 - 1.8101344
Average (Standard dev.)0.026683364 (±0.23573281)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions282828
Spacing282828
CellA=B=C: 193.2 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z6.96.96.9
M x/y/z282828
origin x/y/z0.0000.0000.000
length x/y/z193.200193.200193.200
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ352352352
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS282828
D min/max/mean-0.7581.8100.027

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Supplemental data

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Sample components

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Entire : HeLa cell, interphase

EntireName: HeLa cell, interphase
Components
  • Cell: HeLa cell, interphase

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Supramolecule #1: HeLa cell, interphase

SupramoleculeName: HeLa cell, interphase / type: cell / ID: 1 / Parent: 0 / Details: CCL2-
Source (natural)Organism: Homo sapiens (human) / Organ: cervix

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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 / Details: yeast-extract supplemented
GridModel: Quantifoil R2/2 / Material: GOLD / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsPhase plate: VOLTA PHASE PLATE / Energy filter - Name: GIF Quantum LS / Energy filter - Lower energy threshold: 0 eV / Energy filter - Upper energy threshold: 20 eV
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3838 pixel / Digitization - Dimensions - Height: 3710 pixel / Digitization - Sampling interval: 5.0 µm / Number grids imaged: 1 / Number real images: 61 / Average electron dose: 2.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 14493 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus min: 0.0 µm
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 / Resolution.type: BY AUTHOR / Resolution: 24.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.1) / Number subtomograms used: 448
ExtractionNumber tomograms: 1 / Number images used: 24700 / Reference model: cylinder / Method: template matching / Software - Name: PEET (ver. 1.11)
Final 3D classificationSoftware - Name: RELION (ver. 2.1)
Final angle assignmentType: NOT APPLICABLE
Crystal parametersUnit cell - A: 193.2 Å / Unit cell - B: 193.2 Å / Unit cell - C: 193.2 Å / Unit cell - γ: 90 ° / Unit cell - α: 90 ° / Unit cell - β: 90 ° / Space group: P1

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