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- EMDB-9709: Negative stain electron microscopy of the INO80 actin/Arp module ... -

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Basic information

Entry
Database: EMDB / ID: EMD-9709
TitleNegative stain electron microscopy of the INO80 actin/Arp module state I.
Map data3D reconstruction of the INO80 actin/Arp module state I.
Sample
  • Complex: actin/Arp module
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / negative staining / Resolution: 21.96 Å
AuthorsZhang X / Cai G
Funding support China, 1 items
OrganizationGrant numberCountry
Ministry of Science and Technology (China)2014CB910700 China
CitationJournal: J Mol Cell Biol / Year: 2019
Title: Structure and functional interactions of INO80 actin/Arp module.
Authors: Xuan Zhang / Xuejuan Wang / Zhihui Zhang / Gang Cai /
Abstract: The presence and functions of nuclear actin have been controversial due to the lack of molecular mechanisms. Nuclear actin and actin-related proteins (Arps) are subunits of several chromatin ...The presence and functions of nuclear actin have been controversial due to the lack of molecular mechanisms. Nuclear actin and actin-related proteins (Arps) are subunits of several chromatin remodelers, including the evolutionarily conserved INO80 chromatin-remodeling complex. Here, we present an improved cryo-EM structure of the yeast INO80 complex and the first 3D reconstruction of the INO80 actin/Arp module. The modular and subunit architecture is defined using a combination of subunit deletion analysis and published crosslinking-mass spectrometry. The functional interactions of the INO80 actin/Arp module with a nucleosome is 3D EM reconstructed in two different binding states. Nucleosomes initially bind to the Arp8 subunit and the substantial conformational changes maximize nucleosome contacts of the actin/Arp module, which could promote the bound nucleosome to be engaged onto the INO80 ATPase domain. Our findings suggest that the conserved nuclear actin/Arp module acts a conformational switch of the INO80 for nucleosome binding.
History
DepositionNov 10, 2018-
Header (metadata) releaseOct 16, 2019-
Map releaseOct 16, 2019-
UpdateOct 16, 2019-
Current statusOct 16, 2019Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0375
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.0375
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_9709.png

Downloads & links

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Map

FileDownload / File: emd_9709.map.gz / Format: CCP4 / Size: 2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation3D reconstruction of the INO80 actin/Arp module state I.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
3.54 Å/pix.
x 80 pix.
= 283.2 Å		3.54 Å/pix.
x 80 pix.
= 283.2 Å		3.54 Å/pix.
x 80 pix.
= 283.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 3.54 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0375 / Movie #1: 0.0375
Minimum - Maximum-0.037797775 - 0.10551959
Average (Standard dev.)0.0005840794 (±0.0062889215)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions808080
Spacing808080
CellA=B=C: 283.2 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z3.543.543.54
M x/y/z808080
origin x/y/z0.0000.0000.000
length x/y/z283.200283.200283.200
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS808080
D min/max/mean-0.0380.1060.001

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Supplemental data

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Sample components

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Entire : actin/Arp module

EntireName: actin/Arp module
Components
  • Complex: actin/Arp module

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Supramolecule #1: actin/Arp module

SupramoleculeName: actin/Arp module / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Details: Negative stain electron microscopy of the INO80 actin/Arp module state I.
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

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Experimental details

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Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation statecell

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Sample preparation

BufferpH: 7.5
StainingType: NEGATIVE / Material: Uranyl Formate
VitrificationCryogen name: OTHER

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Electron microscopy

MicroscopeFEI TECNAI F20
Image recordingFilm or detector model: FEI EAGLE (2k x 2k) / Average electron dose: 36.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 21.96 Å / Resolution method: FSC 0.5 CUT-OFF / Number images used: 2218
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING

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