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- EMDB-3925: Nucleosome breathing : Class 9 -

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Basic information

Entry
Database: EMDB / ID: 3925
TitleNucleosome breathing : Class 9
Map dataNucleosome breathing Class 9
SampleNucleosome
SourceXenopus laevis / African clawed frog / amphibia / African clawed frog /
MethodCryo EM / single particle reconstruction / 8.3 Å resolution
AuthorsHalic M / Bilokapic S
CitationJournal: Nat. Struct. Mol. Biol. / Year: 2018
Title: Histone octamer rearranges to adapt to DNA unwrapping.
Authors: Silvija Bilokapic / Mike Strauss / Mario Halic
Abstract: Nucleosomes, the basic units of chromatin, package and regulate expression of eukaryotic genomes. Although the structure of the intact nucleosome is well characterized, little is known about ...Nucleosomes, the basic units of chromatin, package and regulate expression of eukaryotic genomes. Although the structure of the intact nucleosome is well characterized, little is known about structures of partially unwrapped, transient intermediates. In this study, we present nine cryo-EM structures of distinct conformations of nucleosome and subnucleosome particles. These structures show that initial DNA breathing induces conformational changes in the histone octamer, particularly in histone H3, that propagate through the nucleosome and prevent symmetrical DNA opening. Rearrangements in the H2A-H2B dimer strengthen interaction with the unwrapping DNA and promote nucleosome stability. In agreement with this, cross-linked H2A-H2B that cannot accommodate unwrapping of the DNA is not stably maintained in the nucleosome. H2A-H2B release and DNA unwrapping occur simultaneously, indicating that DNA is essential in stabilizing the dimer in the nucleosome. Our structures reveal intrinsic nucleosomal plasticity that is required for nucleosome stability and might be exploited by extrinsic protein factors.
DateDeposition: Oct 13, 2017 / Header (metadata) release: Oct 25, 2017 / Map release: Dec 27, 2017 / Last update: Jan 24, 2018

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.11
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by radius
  • Surface level: 0.11
  • Imaged by UCSF CHIMERA
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3D viewer
Supplemental images

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Map

Fileemd_3925.map.gz (map file in CCP4 format, 18967 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
168 pix
1.4 Å/pix.
= 235.2 Å
168 pix
1.4 Å/pix.
= 235.2 Å
168 pix
1.4 Å/pix.
= 235.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 1.4 Å
Density
Contour Level:0.11 (by author), 0.11 (movie #1):
Minimum - Maximum-0.09999517 - 0.43386328
Average (Standard dev.)0.0024632795 (0.02441921)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions168168168
Origin000
Limit167167167
Spacing168168168
CellA=B=C: 235.2 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.41.41.4
M x/y/z168168168
origin x/y/z0.0000.0000.000
length x/y/z235.200235.200235.200
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS168168168
D min/max/mean-0.1000.4340.002

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Supplemental data

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Sample components

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Entire Nucleosome

EntireName: Nucleosome / Number of components: 1
MassTheoretical: 200 kDa

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Component #1: protein, Nucleosome

ProteinName: Nucleosome / Recombinant expression: No
MassTheoretical: 200 kDa
SourceSpecies: Xenopus laevis / African clawed frog / amphibia / African clawed frog /
Source (engineered)Expression System: Escherichia coli / / bacteria /

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: Cryo EM
Sample solutionpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

ImagingMicroscope: FEI TITAN
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 100 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: FEI FALCON II (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 9000
3D reconstructionSoftware: RELION / Resolution: 8.3 Å / Resolution method: FSC 0.143 CUT-OFF

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