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- EMDB-3925: Nucleosome breathing : Class 9 -

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Basic information

Database: EMDB / ID: EMD-3925
TitleNucleosome breathing : Class 9
Map dataNucleosome breathing Class 9
  • Complex: Nucleosome
Biological speciesXenopus laevis (African clawed frog)
Methodsingle particle reconstruction / cryo EM / Resolution: 8.3 Å
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.
DepositionOct 13, 2017-
Header (metadata) releaseOct 25, 2017-
Map releaseDec 27, 2017-
UpdateJan 24, 2018-
Current statusJan 24, 2018Processing site: PDBe / Status: Released

Structure visualization

  • Surface view with section colored by density value
  • Surface level: 0.11
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.11
  • Imaged by UCSF Chimera
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Structure viewerEM map:
Supplemental images

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FileDownload / File: emd_3925.map.gz / Format: CCP4 / Size: 18.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationNucleosome breathing Class 9
Projections & slices

Image control

AxesZ (Sec.)Y (Row.)X (Col.)
1.4 Å/pix.
x 168 pix.
= 235.2 Å
1.4 Å/pix.
x 168 pix.
= 235.2 Å
1.4 Å/pix.
x 168 pix.
= 235.2 Å



Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.4 Å
Contour LevelBy AUTHOR: 0.11 / Movie #1: 0.11
Minimum - Maximum-0.09999517 - 0.43386328
Average (Standard dev.)0.0024632795 (±0.02441921)
SymmetrySpace group: 1


Map geometry
Axis orderXYZ
CellA=B=C: 235.2 Å
α=β=γ: 90.0 °

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
MAP C/R/S123
start NC/NR/NS000
D min/max/mean-0.1000.4340.002

Supplemental data

Sample components

Entire : Nucleosome

EntireName: Nucleosome
  • Complex: Nucleosome

Supramolecule #1: Nucleosome

SupramoleculeName: Nucleosome / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Xenopus laevis (African clawed frog)
Recombinant expressionOrganism: Escherichia coli (E. coli)
Molecular weightTheoretical: 200 KDa

Experimental details

Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

Electron microscopy

MicroscopeFEI TITAN
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Detector mode: INTEGRATING / Average electron dose: 100.0 e/Å2

Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 8.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 1.4) / Number images used: 9000

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