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- EMDB-22794: Alpha2-macroglobulin family protein isolated from interphase chro... -

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Basic information

Entry
Database: EMDB / ID: EMD-22794
TitleAlpha2-macroglobulin family protein isolated from interphase chromosome formed in Xenopus egg extract
Map dataAlpha2-macroglobulin family protein isolated from interphase chromosome formed in Xenopus egg extract
Sample
  • Complex: alpha2-macroglobulin isolated from interphase chromosome formed in Xenopus egg extract
Biological speciesXenopus laevis (African clawed frog)
Methodsingle particle reconstruction / cryo EM / Resolution: 8.07 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: 0.4
  • 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

emd_22794.png

Downloads & links

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Map

FileDownload / File: emd_22794.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationAlpha2-macroglobulin family protein isolated from interphase chromosome formed in Xenopus egg extract
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

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.4 / Movie #1: 0.4
Minimum - Maximum-0.21017519 - 0.84563893
Average (Standard dev.)0.00068195537 (±0.05010915)
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
start NX/NY/NZ000
NX/NY/NZ376376376
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-0.2100.8460.001

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Supplemental data

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Mask #1

Fileemd_22794_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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

Fileemd_22794_half_map_1.map
AnnotationAlpha2-macroglobulin family protein isolated from interphase chromosome formed in Xenopus egg extract
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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

Fileemd_22794_half_map_2.map
AnnotationAlpha2-macroglobulin family protein isolated from interphase chromosome formed in Xenopus egg extract
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : alpha2-macroglobulin isolated from interphase chromosome formed i...

EntireName: alpha2-macroglobulin isolated from interphase chromosome formed in Xenopus egg extract
Components
  • Complex: alpha2-macroglobulin isolated from interphase chromosome formed in Xenopus egg extract

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Supramolecule #1: alpha2-macroglobulin isolated from interphase chromosome formed i...

SupramoleculeName: alpha2-macroglobulin isolated from interphase chromosome formed in Xenopus egg extract
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6
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 TALOS ARCTICA
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 33.11 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 8.07 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3) / Number images used: 9721
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 3)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model(PDB ID:

6dzt

,

5nl0

)

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