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- EMDB-1781: The nucleosome organization in 30nm fiber -

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Open data


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Basic information

Entry
Database: EMDB / ID: EMD-1781
TitleThe nucleosome organization in 30nm fiber
Map datasub-tomogram average
Sample
  • Sample: 30nm fiber
  • Protein or peptide: 30-nm fiber
Keywords30nm fiber
Biological speciesGallus gallus (chicken)
Methodsubtomogram averaging / cryo EM / Resolution: 43.1 Å
AuthorsScheffer MP / Eltsov M / Frangakis AS
CitationJournal: Proc Natl Acad Sci U S A / Year: 2011
Title: Evidence for short-range helical order in the 30-nm chromatin fibers of erythrocyte nuclei.
Authors: Margot P Scheffer / Mikhail Eltsov / Achilleas S Frangakis /
Abstract: Chromatin folding in eukaryotes fits the genome into the limited volume of the cell nucleus. Formation of higher-order chromatin structures attenuates DNA accessibility, thus contributing to the ...Chromatin folding in eukaryotes fits the genome into the limited volume of the cell nucleus. Formation of higher-order chromatin structures attenuates DNA accessibility, thus contributing to the control of essential genome functions such as transcription, DNA replication, and repair. The 30-nm fiber is thought to be the first hierarchical level of chromatin folding, but the nucleosome arrangement in the compact 30-nm fiber was previously unknown. We used cryoelectron tomography of vitreous sections to determine the structure of the compact, native 30-nm fiber of avian erythrocyte nuclei. The predominant geometry of the 30-nm fiber revealed by subtomogram averaging is a left-handed two-start helix with approximately 6.5 nucleosomes per 11 nm, in which the nucleosomes are juxtaposed face-to-face but are shifted off their superhelical axes with an axial translation of approximately 3.4 nm and an azimuthal rotation of approximately 54°. The nucleosomes produce a checkerboard pattern when observed in the direction perpendicular to the fiber axis but are not interdigitated. The nucleosome packing within the fibers shows larger center-to-center internucleosomal distances than previously anticipated, thus excluding the possibility of core-to-core interactions, explaining how transcription and regulation factors can access nucleosomes.
History
DepositionSep 8, 2010-
Header (metadata) releaseSep 26, 2012-
Map releaseSep 26, 2012-
UpdateDec 11, 2013-
Current statusDec 11, 2013Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: -4.034770368
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: -4.034770368
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

EMD-1781.png

Downloads & links

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Map

FileDownload / File: emd_1781.map.gz / Format: CCP4 / Size: 1001 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsub-tomogram average
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
12 Å/pix.
x 64 pix.
= 768. Å		12 Å/pix.
x 64 pix.
= 768. Å		12 Å/pix.
x 64 pix.
= 768. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 12 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy EMDB: 1.5 / Movie #1: -4.0347704
Minimum - Maximum-9.352617260000001 - 3.72104096
Average (Standard dev.)0.06343354 (±1.2620393)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions646464
Spacing646464
CellA=B=C: 768.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z121212
M x/y/z646464
origin x/y/z0.0000.0000.000
length x/y/z768.000768.000768.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-184-184-183
NX/NY/NZ368368368
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS646464
D min/max/mean-9.3533.7210.063

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Supplemental data

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Sample components

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Entire : 30nm fiber

EntireName: 30nm fiber
Components
  • Sample: 30nm fiber
  • Protein or peptide: 30-nm fiber

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Supramolecule #1000: 30nm fiber

SupramoleculeName: 30nm fiber / type: sample / ID: 1000 / Number unique components: 1

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Macromolecule #1: 30-nm fiber

MacromoleculeName: 30-nm fiber / type: protein_or_peptide / ID: 1 / Name.synonym: 30-nm fiber / Recombinant expression: No / Database: NCBI
Source (natural)Organism: Gallus gallus (chicken) / synonym: Chicken / Location in cell: nucleus

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging

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Sample preparation

VitrificationCryogen name: NITROGEN / Instrument: OTHER

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Electron microscopy

MicroscopeFEI POLARA 300
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD
Sample stageSpecimen holder: Eucentric / Specimen holder model: OTHER
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 43.1 Å / Resolution method: FSC 0.5 CUT-OFF

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