[English] 日本語
Yorodumi
- EMDB-9712: Negative stain electron microscopy of the actin/Arp-Nucleosome as... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-9712
TitleNegative stain electron microscopy of the actin/Arp-Nucleosome assembly state II.
Map data3D reconstruction of the actin/Arp-Nucleosome assembly state II.
Sample
  • Complex: actin/Arp-Nucleosome assembly
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / negative staining / Resolution: 27.493 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 11, 2018-
Header (metadata) releaseOct 16, 2019-
Map releaseOct 16, 2019-
UpdateOct 16, 2019-
Current statusOct 16, 2019Processing site: PDBj / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.898
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.898
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_9712.png

Downloads & links

-
Map

FileDownload / File: emd_9712.map.gz / Format: CCP4 / Size: 6.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation3D reconstruction of the actin/Arp-Nucleosome assembly state II.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
3.54 Å/pix.
x 120 pix.
= 424.8 Å		3.54 Å/pix.
x 120 pix.
= 424.8 Å		3.54 Å/pix.
x 120 pix.
= 424.8 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: 0.898 / Movie #1: 0.898
Minimum - Maximum-0.8858642 - 2.3721907
Average (Standard dev.)0.012686897 (±0.17037803)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-60-60-60
Dimensions120120120
Spacing120120120
CellA=B=C: 424.8 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z3.543.543.54
M x/y/z120120120
origin x/y/z0.0000.0000.000
length x/y/z424.800424.800424.800
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-60-60-60
NC/NR/NS120120120
D min/max/mean-0.8862.3720.013

-
Supplemental data

-
Sample components

-
Entire : actin/Arp-Nucleosome assembly

EntireName: actin/Arp-Nucleosome assembly
Components
  • Complex: actin/Arp-Nucleosome assembly

-
Supramolecule #1: actin/Arp-Nucleosome assembly

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

-
Experimental details

-
Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation statecell

-
Sample preparation

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

-
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

-
Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 27.493 Å / Resolution method: FSC 0.5 CUT-OFF / Number images used: 1157
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more