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- EMDB-6737: Natural chromatin is heterogeneous and self associates in vitro -

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Basic information

Entry
Database: EMDB / ID: EMD-6737
TitleNatural chromatin is heterogeneous and self associates in vitro
Map dataCryotomogram of picoplankton chromatin in 5mM EDTA.
Sample
  • Organelle or cellular component: Chromatin released from the picoplankton Ostreococcus tauri, in 5mM EDTA
Biological speciesOstreococcus tauri (plant)
Methodelectron tomography / cryo EM
AuthorsCai S / Song Y / Chen C / Shi J / Gan L
CitationJournal: Mol Biol Cell / Year: 2018
Title: Natural chromatin is heterogeneous and self-associates in vitro.
Authors: Shujun Cai / Yajiao Song / Chen Chen / Jian Shi / Lu Gan /
Abstract: The 30-nm fiber is commonly formed by oligonucleosome arrays in vitro but rarely found inside cells. To determine how chromatin higher-order structure is controlled, we used electron cryotomography ...The 30-nm fiber is commonly formed by oligonucleosome arrays in vitro but rarely found inside cells. To determine how chromatin higher-order structure is controlled, we used electron cryotomography (cryo-ET) to study the undigested natural chromatin released from two single-celled organisms in which 30-nm fibers have not been observed in vivo: picoplankton and yeast. In the presence of divalent cations, most of the chromatin from both organisms is condensed into a large mass in vitro. Rare irregular 30-nm fibers, some of which include face-to-face nucleosome interactions, do form at the periphery of this mass. In the absence of divalent cations, picoplankton chromatin decondenses into open zigzags. By contrast, yeast chromatin mostly remains condensed, with very few open motifs. Yeast chromatin packing is largely unchanged in the absence of linker histone and mildly decondensed when histones are more acetylated. Natural chromatin is therefore generally nonpermissive of regular motifs, even at the level of oligonucleosomes.
History
DepositionMay 18, 2017-
Header (metadata) releaseMay 23, 2018-
Map releaseMay 23, 2018-
UpdateMay 23, 2018-
Current statusMay 23, 2018Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Solid view (volume rendering)
  • Imaged by UCSF Chimera
  • Download
  • Solid view (volume rendering)
  • Imaged by UCSF Chimera
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Supplemental images

emd_6737.png

Downloads & links

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Map

FileDownload / File: emd_6737.map.gz / Format: CCP4 / Size: 1.1 GB / Type: IMAGE STORED AS SIGNED INTEGER (2 BYTES)
AnnotationCryotomogram of picoplankton chromatin in 5mM EDTA.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
9.12 Å/pix.
x 174 pix.
= 1586.88 Å		9.12 Å/pix.
x 1238 pix.
= 11290.56 Å		9.12 Å/pix.
x 2807 pix.
= 25599.84 Å

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 9.12 Å
Density

Histogram

Histogram (log scale)
Minimum - Maximum-6665. - 5158.
Average (Standard dev.)210.984970000000004 (±153.699569999999994)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-2855-82279
Dimensions12382807174
Spacing28071238174
CellA: 25599.84 Å / B: 11290.56 Å / C: 1586.88 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Integer*27
Å/pix. X/Y/Z9.129.129.12
M x/y/z28071238174
origin x/y/z0.0000.0000.000
length x/y/z25599.84011290.5601586.880
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-822-285579
NC/NR/NS28071238174
D min/max/mean-6665.0005158.000210.985

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Supplemental data

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Additional map: Cryotomogram of yeast chromatin in 50mM EDTA.

Fileemd_6737_additional.map
AnnotationCryotomogram of yeast chromatin in 50mM EDTA.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Chromatin released from the picoplankton Ostreococcus tauri, in 5...

EntireName: Chromatin released from the picoplankton Ostreococcus tauri, in 5mM EDTA
Components
  • Organelle or cellular component: Chromatin released from the picoplankton Ostreococcus tauri, in 5mM EDTA

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Supramolecule #1: Chromatin released from the picoplankton Ostreococcus tauri, in 5...

SupramoleculeName: Chromatin released from the picoplankton Ostreococcus tauri, in 5mM EDTA
type: organelle_or_cellular_component / ID: 1 / Parent: 0
Source (natural)Organism: Ostreococcus tauri (plant) / Strain: RCC 745

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Experimental details

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Structure determination

Methodcryo EM
Processingelectron tomography
Aggregation statefilament

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Sample preparation

BufferpH: 7
Component:
ConcentrationName
20.0 mMHEPES
144.0 mMSucrose
6.0 %Glycerol
5.0 mMEDTA
1.0 xProtease inhibitor cocktail, EDTA free
GridModel: Protochips CF-4/2-2C-T / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: PLASMA CLEANING / Details: 15mA, Emitech K100X
VitrificationCryogen name: NITROGEN / Chamber humidity: 100 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV
SectioningOther: NO SECTIONING
Fiducial markerManufacturer: Sigma / Diameter: 10 nm

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Detector mode: INTEGRATING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number grids imaged: 1 / Number real images: 62 / Average electron dose: 2.4 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated defocus min: 11.0 µm / Calibrated magnification: 15678 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus min: 8.0 µm / Nominal magnification: 8700
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 reconstructionAlgorithm: BACK PROJECTION / Software - Name: IMOD (ver. 4.9) / Number images used: 59
CTF correctionSoftware - Name: IMOD (ver. 4.8)

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