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- EMDB-22792: H1.8 bound nucleosome isolated from metaphase chromosome in Xenop... -

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Basic information

Entry
Database: EMDB / ID: EMD-22792
TitleH1.8 bound nucleosome isolated from metaphase chromosome in Xenopus egg extract (oligo fraction)
Map data
SampleH1.8 bound nucleosome isolated from metaphase chromosome in Xenopus egg extract (oligo fraction):
Histone H3.2 / Histone H4 / Histone H2A / Histone H2B 1.1 / (nucleic-acidNucleic acid) x 2 / Protein B4
Function / homology
Function and homology information


DNA-templated transcription, initiation / nucleosome assembly / nucleosome / multicellular organism development / protein heterodimerization activity / DNA binding / nucleoplasm / nucleus
Similarity search - Function
linker histone H1 and H5 family / Linker histone H1/H5 globular (H15) domain profile. / Domain in histone families 1 and 5 / Linker histone H1/H5, domain H15 / Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A signature. / Histone H2A conserved site / C-terminus of histone H2A ...linker histone H1 and H5 family / Linker histone H1/H5 globular (H15) domain profile. / Domain in histone families 1 and 5 / Linker histone H1/H5, domain H15 / Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A signature. / Histone H2A conserved site / C-terminus of histone H2A / Histone H2A, C-terminal domain / Histone 2A / Histone H2A / Histone H4 signature. / Histone H4, conserved site / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF) / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Core histone H2A/H2B/H3/H4 / Histone H2A/H2B/H3 / Histone-fold / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
Histone H2B 1.1 / Protein B4 / Histone H4 / Histone H3.2 / Histone H2A
Similarity search - Component
Biological speciesXenopus laevis (African clawed frog) / African clawed frog (African clawed frog)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.42 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-
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: 0.2
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.2
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-7kbf
  • Surface level: 0.2
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_22792.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.47 Å/pix.
x 200 pix.
= 294. Å
1.47 Å/pix.
x 200 pix.
= 294. Å
1.47 Å/pix.
x 200 pix.
= 294. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.47 Å
Density
Contour LevelBy AUTHOR: 0.2 / Movie #1: 0.2
Minimum - Maximum-1.0565802 - 1.7124438
Average (Standard dev.)0.00093330065 (±0.063368164)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 294.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.471.471.47
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z294.000294.000294.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS200200200
D min/max/mean-1.0571.7120.001

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Supplemental data

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Additional map: The map without flipping and rescaling

Fileemd_22792_additional_1.map
AnnotationThe map without flipping and rescaling
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Half map: H1.8 bound nucleosome isolated from metaphase chromosome in...

Fileemd_22792_half_map_1.map
AnnotationH1.8 bound nucleosome isolated from metaphase chromosome in Xenopus egg extract (oligo fraction)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Half map: H1.8 bound nucleosome isolated from metaphase chromosome in...

Fileemd_22792_half_map_2.map
AnnotationH1.8 bound nucleosome isolated from metaphase chromosome in Xenopus egg extract (oligo fraction)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Sample components

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Entire H1.8 bound nucleosome isolated from metaphase chromosome in Xenop...

EntireName: H1.8 bound nucleosome isolated from metaphase chromosome in Xenopus egg extract (oligo fraction)
Number of Components: 8

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Component #1: protein, H1.8 bound nucleosome isolated from metaphase chromosome...

ProteinName: H1.8 bound nucleosome isolated from metaphase chromosome in Xenopus egg extract (oligo fraction)
Recombinant expression: No
SourceSpecies: Xenopus laevis (African clawed frog)

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Component #2: protein, Histone H3.2

ProteinName: Histone H3.2 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 15.421101 kDa
SourceSpecies: African clawed frog (African clawed frog)

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Component #3: protein, Histone H4

ProteinName: Histone H4 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 11.394426 kDa
SourceSpecies: African clawed frog (African clawed frog)

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Component #4: protein, Histone H2A

ProteinName: Histone H2A / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 14.883174 kDa
SourceSpecies: African clawed frog (African clawed frog)

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Component #5: protein, Histone H2B 1.1

ProteinName: Histone H2B 1.1 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 13.965265 kDa
SourceSpecies: African clawed frog (African clawed frog)

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Component #6: nucleic-acid, DNA (184-MER)

nucleic acidName: DNA (184-MER) / Class: DNA / Structure: OTHER / Synthetic: No
Sequence: (DT)(DT)(DG)(DG)(DC)(DC)(DA)(DG)(DC)(DT) (DA)(DG)(DG)(DA)(DT)(DA)(DT)(DC)(DA)(DC) (DA)(DA)(DT)(DC)(DC)(DC)(DG)(DG)(DT)(DG) (DC)(DC)(DG)(DA)(DG)(DG)(DC)(DC)(DG)(DC) (DT)(DC)(DA)(DA)(DT)(DT) ...Sequence:
(DT)(DT)(DG)(DG)(DC)(DC)(DA)(DG)(DC)(DT) (DA)(DG)(DG)(DA)(DT)(DA)(DT)(DC)(DA)(DC) (DA)(DA)(DT)(DC)(DC)(DC)(DG)(DG)(DT)(DG) (DC)(DC)(DG)(DA)(DG)(DG)(DC)(DC)(DG)(DC) (DT)(DC)(DA)(DA)(DT)(DT)(DG)(DG)(DT)(DC) (DG)(DT)(DA)(DG)(DA)(DC)(DA)(DG)(DC)(DT) (DC)(DT)(DA)(DG)(DC)(DA)(DC)(DC)(DG)(DC) (DT)(DT)(DA)(DA)(DA)(DC)(DG)(DC)(DA)(DC) (DG)(DT)(DA)(DC)(DG)(DG)(DA)(DA)(DT)(DC) (DC)(DG)(DT)(DA)(DC)(DG)(DT)(DG)(DC)(DG) (DT)(DT)(DT)(DA)(DA)(DG)(DC)(DG)(DG)(DT) (DG)(DC)(DT)(DA)(DG)(DA)(DG)(DC)(DT)(DG) (DT)(DC)(DT)(DA)(DC)(DG)(DA)(DC)(DC)(DA) (DA)(DT)(DT)(DG)(DA)(DG)(DC)(DG)(DG)(DC) (DC)(DT)(DC)(DG)(DG)(DC)(DA)(DC)(DC)(DG) (DG)(DG)(DA)(DT)(DT)(DG)(DT)(DG)(DA)(DT) (DA)(DT)(DC)(DC)(DT)(DA)(DG)(DC)(DT)(DG) (DG)(DC)
MassTheoretical: 53.114832 kDa
SourceSpecies: African clawed frog (African clawed frog)

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Component #7: nucleic-acid, DNA (184-MER)

nucleic acidName: DNA (184-MER) / Class: DNA / Structure: OTHER / Synthetic: No
Sequence: (DG)(DC)(DC)(DA)(DG)(DC)(DT)(DA)(DG)(DG) (DA)(DT)(DA)(DT)(DC)(DA)(DC)(DA)(DA)(DT) (DC)(DC)(DC)(DG)(DG)(DT)(DG)(DC)(DC)(DG) (DA)(DG)(DG)(DC)(DC)(DG)(DC)(DT)(DC)(DA) (DA)(DT)(DT)(DG)(DG)(DT) ...Sequence:
(DG)(DC)(DC)(DA)(DG)(DC)(DT)(DA)(DG)(DG) (DA)(DT)(DA)(DT)(DC)(DA)(DC)(DA)(DA)(DT) (DC)(DC)(DC)(DG)(DG)(DT)(DG)(DC)(DC)(DG) (DA)(DG)(DG)(DC)(DC)(DG)(DC)(DT)(DC)(DA) (DA)(DT)(DT)(DG)(DG)(DT)(DC)(DG)(DT)(DA) (DG)(DA)(DC)(DA)(DG)(DC)(DT)(DC)(DT)(DA) (DG)(DC)(DA)(DC)(DC)(DG)(DC)(DT)(DT)(DA) (DA)(DA)(DC)(DG)(DC)(DA)(DC)(DG)(DT)(DA) (DC)(DG)(DG)(DA)(DT)(DT)(DC)(DC)(DG)(DT) (DA)(DC)(DG)(DT)(DG)(DC)(DG)(DT)(DT)(DT) (DA)(DA)(DG)(DC)(DG)(DG)(DT)(DG)(DC)(DT) (DA)(DG)(DA)(DG)(DC)(DT)(DG)(DT)(DC)(DT) (DA)(DC)(DG)(DA)(DC)(DC)(DA)(DA)(DT)(DT) (DG)(DA)(DG)(DC)(DG)(DG)(DC)(DC)(DT)(DC) (DG)(DG)(DC)(DA)(DC)(DC)(DG)(DG)(DG)(DA) (DT)(DT)(DG)(DT)(DG)(DA)(DT)(DA)(DT)(DC) (DC)(DT)(DA)(DG)(DC)(DT)(DG)(DG)(DC)(DC) (DA)(DA)
MassTheoretical: 53.083816 kDa
SourceSpecies: African clawed frog (African clawed frog)

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Component #8: protein, Protein B4

ProteinName: Protein B4 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 29.387369 kDa
SourceSpecies: African clawed frog (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 / Number of Projections: 27383
3D reconstructionSoftware: cryoSPARC / Resolution: 4.42 Å / Resolution Method: FSC 0.143 CUT-OFF
FSC plot (resolution estimation)

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Atomic model buiding

Modeling #1Input PDB model: 6DZT, 5NL0
Output model

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