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- EMDB-22796: Alpha2-macroglobulin family protein isolated from metaphase chrom... -

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Basic information

Entry
Database: EMDB / ID: EMD-22796
TitleAlpha2-macroglobulin family protein isolated from metaphase chromosome formed in Xenopus egg extract
Map data
Samplenucleosome isolated from metaphase chromosome formed in Xenopus egg extract (oligo fraction)
Biological speciesXenopus laevis (African clawed frog)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.5 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 2, 2020-
Header (metadata) releaseSep 15, 2021-
Map releaseSep 15, 2021-
UpdateSep 15, 2021-
Current statusSep 15, 2021Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.4
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.4
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_22796.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.5 Å/pix.
x 320 pix.
= 480. Å
1.5 Å/pix.
x 320 pix.
= 480. Å
1.5 Å/pix.
x 320 pix.
= 480. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.5 Å
Density
Contour LevelBy AUTHOR: 0.4 / Movie #1: 0.4
Minimum - Maximum-0.18895288 - 0.9532032
Average (Standard dev.)0.0014944029 (±0.04844508)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 480.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.51.51.5
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z480.000480.000480.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-0.1890.9530.001

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Supplemental data

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Segmentation: #1

Fileemd_22796_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Half map: Alpha2-macroglobulin family protein isolated from metaphase chromosome formed...

Fileemd_22796_half_map_1.map
AnnotationAlpha2-macroglobulin family protein isolated from metaphase chromosome formed in Xenopus egg extract
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Half map: Alpha2-macroglobulin family protein isolated from metaphase chromosome formed...

Fileemd_22796_half_map_2.map
AnnotationAlpha2-macroglobulin family protein isolated from metaphase chromosome formed in Xenopus egg extract
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Sample components

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Entire nucleosome isolated from metaphase chromosome formed in Xenopus e...

EntireName: nucleosome isolated from metaphase chromosome formed in Xenopus egg extract (oligo fraction)
Number of Components: 1

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Component #1: protein, nucleosome isolated from metaphase chromosome formed in ...

ProteinName: nucleosome isolated from metaphase chromosome formed in Xenopus egg extract (oligo fraction)
Recombinant expression: No
SourceSpecies: Xenopus laevis (African clawed frog)

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Experimental details

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Sample preparation

SpecimenSpecimen State: Particle / Method: cryo EM
Sample solutionpH: 7.4
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen Name: ETHANE / Temperature: 277 K / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
ImagingMicroscope: FEI TALOS ARCTICA
Electron gunElectron Source: FIELD EMISSION GUN / Accelerating Voltage: 200 kV / Electron Dose: 35.27 e/Å2 / Illumination Mode: FLOOD BEAM
LensImaging Mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Applied Symmetry: D2 (2x2 fold dihedral) / Number of Projections: 49363
3D reconstructionSoftware: cryoSPARC / Resolution: 5.5 Å / Resolution Method: FSC 0.143 CUT-OFF
FSC plot (resolution estimation)

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