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- EMDB-22797: Nucleosome isolated from interphase chromosome formed in Xenopus ... -

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Basic information

Entry
Database: EMDB / ID: EMD-22797
TitleNucleosome isolated from interphase chromosome formed in Xenopus egg extract (mono fraction)
Map dataFliped and rescaled map
Sample
  • Complex: Nucleosome in interphase chromosome formed in Xenopus egg extract (oligo fraction)
Function / homology
Function and homology information


structural constituent of chromatin / nucleosome / heterochromatin formation / nucleosome assembly / protein heterodimerization activity / DNA binding / nucleoplasm / nucleus
Similarity search - Function
: / Histone H2B signature. / Histone H2A conserved site / Histone H2A signature. / Histone H2B / Histone H2B / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone 2A / Histone H2A ...: / Histone H2B signature. / Histone H2A conserved site / Histone H2A signature. / Histone H2B / Histone H2B / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone 2A / Histone H2A / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 domain / Histone-fold
Similarity search - Domain/homology
Histone H2B 1.1 / Histone H4 / Histone H3.2 / Histone H2A
Similarity search - Component
Biological speciesXenopus laevis (African clawed frog)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.12 Å
AuthorsArimura Y / Funabiki H
Funding support United States, Japan, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM132111 United States
Japan Society for the Promotion of Science (JSPS)JSPS Overseas Research Fellowships Japan
CitationJournal: Mol Cell / Year: 2021
Title: Structural features of nucleosomes in interphase and metaphase chromosomes.
Authors: Yasuhiro Arimura / Rochelle M Shih / Ruby Froom / Hironori Funabiki /
Abstract: Structural heterogeneity of nucleosomes in functional chromosomes is unknown. Here, we devise the template-, reference- and selection-free (TRSF) cryo-EM pipeline to simultaneously reconstruct cryo- ...Structural heterogeneity of nucleosomes in functional chromosomes is unknown. Here, we devise the template-, reference- and selection-free (TRSF) cryo-EM pipeline to simultaneously reconstruct cryo-EM structures of protein complexes from interphase or metaphase chromosomes. The reconstructed interphase and metaphase nucleosome structures are on average indistinguishable from canonical nucleosome structures, despite DNA sequence heterogeneity, cell-cycle-specific posttranslational modifications, and interacting proteins. Nucleosome structures determined by a decoy-classifying method and structure variability analyses reveal the nucleosome structural variations in linker DNA, histone tails, and nucleosome core particle configurations, suggesting that the opening of linker DNA, which is correlated with H2A C-terminal tail positioning, is suppressed in chromosomes. High-resolution (3.4-3.5 Å) nucleosome structures indicate DNA-sequence-independent stabilization of superhelical locations ±0-1 and ±3.5-4.5. The linker histone H1.8 preferentially binds to metaphase chromatin, from which chromatosome cryo-EM structures with H1.8 at the on-dyad position are reconstituted. This study presents the structural characteristics of nucleosomes in chromosomes.
History
DepositionOct 3, 2020-
Header (metadata) releaseSep 15, 2021-
Map releaseSep 15, 2021-
UpdateNov 17, 2021-
Current statusNov 17, 2021Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.014
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.014
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_22797.png

Downloads & links

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Map

FileDownload / File: emd_22797.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFliped and rescaled map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.3 Å/pix.
x 256 pix.
= 332.8 Å		1.3 Å/pix.
x 256 pix.
= 332.8 Å		1.3 Å/pix.
x 256 pix.
= 332.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.3 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.014 / Movie #1: 0.014
Minimum - Maximum-0.020784728 - 0.05805235
Average (Standard dev.)2.1400361e-05 (±0.0023278124)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 332.8 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.31.31.3
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z332.800332.800332.800
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ376376376
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.0210.0580.000

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Supplemental data

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Additional map: 3D classification output map for structural variation analysis

Fileemd_22797_additional_1.map
Annotation3D classification output map for structural variation analysis
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Additional map: 3D classification output map for structural variation analysis

Fileemd_22797_additional_2.map
Annotation3D classification output map for structural variation analysis
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Additional map: 3D classification output map for structural variation analysis

Fileemd_22797_additional_3.map
Annotation3D classification output map for structural variation analysis
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Additional map: 3D classification output map for structural variation analysis

Fileemd_22797_additional_4.map
Annotation3D classification output map for structural variation analysis
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Additional map: 3D classification output map for structural variation analysis

Fileemd_22797_additional_5.map
Annotation3D classification output map for structural variation analysis
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Additional map: 3D classification output map for structural variation analysis

Fileemd_22797_additional_6.map
Annotation3D classification output map for structural variation analysis
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Additional map: The map before flipping

Fileemd_22797_additional_7.map
AnnotationThe map before flipping
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Half map: #1

Fileemd_22797_half_map_1.map
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Half map: #2

Fileemd_22797_half_map_2.map
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Sample components

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Entire : Nucleosome in interphase chromosome formed in Xenopus egg extract...

EntireName: Nucleosome in interphase chromosome formed in Xenopus egg extract (oligo fraction)
Components
  • Complex: Nucleosome in interphase chromosome formed in Xenopus egg extract (oligo fraction)

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Supramolecule #1: Nucleosome in interphase chromosome formed in Xenopus egg extract...

SupramoleculeName: Nucleosome in interphase chromosome formed in Xenopus egg extract (oligo fraction)
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Xenopus laevis (African clawed frog)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
Component:
ConcentrationNameFormula
10.0 mMHEPES-KOH
30.0 mMKClKCl
1.0 mMEGTAEGTA
0.3 microg/mlLeupeptin
0.3 microg/mlPepstatin
0.3 microg/mlChymostatin
1.0 mMSodium Butyrate
1.0 mMbeta-glycerophosphate
1.0 %trehalose
0.1 %1,6,-hexanediol
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 45.02 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 5.12 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3) / Number images used: 13798
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 3)
FSC plot (resolution estimation)

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