[English] 日本語
- EMDB-4278: CryoEM structure of INO80core Nucleosome complex in closed grappl... -

Open data

ID or keywords:


no data

Basic information

Database: EMDB / ID: 4278
TitleCryoEM structure of INO80core Nucleosome complex in closed grappler conformation
Map data
SampleINO80core Nucleosome complex:
Function / homologyINO80 complex, subunit Ies2 / Histone H2A/H2B/H3 / Histone H2A, C-terminal domain / INO80 complex, subunit Ies6 / Actin-related protein 5 / P-loop containing nucleoside triphosphate hydrolase / RuvB-like / Histone H4, conserved site / DASH complex subunit Dad4 / Vps72/YL1, C-terminal ...INO80 complex, subunit Ies2 / Histone H2A/H2B/H3 / Histone H2A, C-terminal domain / INO80 complex, subunit Ies6 / Actin-related protein 5 / P-loop containing nucleoside triphosphate hydrolase / RuvB-like / Histone H4, conserved site / DASH complex subunit Dad4 / Vps72/YL1, C-terminal / TIP49, P-loop domain / Histone-fold / INO80 complex subunit B-like conserved region / CENP-T/Histone H4, histone fold / TATA box binding protein associated factor (TAF) / Actin family / AAA+ ATPase domain / Histone H2A / Histone H4 / Histone H2B / Histone H3/CENP-A / Condensation of Prophase Chromosomes / Oxidative Stress Induced Senescence / Senescence-Associated Secretory Phenotype (SASP) / Histone H2A conserved site / RuvB-like helicase 1 / PRC2 methylates histones and DNA / Histone H3 signature 2. / Pre-NOTCH Transcription and Translation / Packaging Of Telomere Ends / Interleukin-7 signaling / Meiotic synapsis / Metalloprotease DUBs / Ub-specific processing proteases / UCH proteinases / RMTs methylate histone arginines / HATs acetylate histones / HDACs deacetylate histones / Histone H2B signature. / RuvB-like helicase 2 / Histone H3 signature 1. / Histone H4 signature. / Histone H2A signature. / C-terminus of histone H2A / Centromere kinetochore component CENP-T histone fold / DASH complex subunit Dad4 / YL1 nuclear protein C-terminal domain / TIP49 P-loop domain / PAPA-1-like conserved region / Core histone H2A/H2B/H3/H4 / Actin / DNA Damage/Telomere Stress Induced Senescence / HDACs deacetylate histones / PKMTs methylate histone lysines / Deposition of new CENPA-containing nucleosomes at the centromere / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / UCH proteinases / Ub-specific processing proteases / Metalloprotease DUBs / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / Nonhomologous End-Joining (NHEJ) / Processing of DNA double-strand break ends / G2/M DNA damage checkpoint / B-WICH complex positively regulates rRNA expression / RNA Polymerase I Promoter Opening / RNA Polymerase I Chain Elongation / E3 ubiquitin ligases ubiquitinate target proteins / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Estrogen-dependent gene expression / Meiotic recombination / Amyloid fiber formation / Factors involved in megakaryocyte development and platelet production / DNA methylation / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / SUMOylation of chromatin organization proteins / HDMs demethylate histones / NoRC negatively regulates rRNA expression / HATs acetylate histones / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / SIRT1 negatively regulates rRNA expression / RMTs methylate histone arginines / Chromatin modifying enzymes / DASH complex / attachment of spindle microtubules to kinetochore / R2TP complex / Swr1 complex / histone exchange / ATP-dependent 5'-3' DNA helicase activity / nuclear telomeric heterochromatin / Ino80 complex / ATP-dependent 3'-5' DNA helicase activity / NuA4 histone acetyltransferase complex / box C/D snoRNP assembly / negative regulation of megakaryocyte differentiation / CENP-A containing nucleosome assembly / DNA replication-independent nucleosome assembly / telomere capping
Function and homology information
SourceChaetomium thermophilum var. thermophilum DSM 1495 (fungus)
Methodsingle particle reconstruction / cryo EM / 4.68 Å resolution
AuthorsEustermann S / Schall K / Strauss M / Hopnfer KP
CitationJournal: Nature / Year: 2018
Title: Structural basis for ATP-dependent chromatin remodelling by the INO80 complex.
Authors: Sebastian Eustermann / Kevin Schall / Dirk Kostrewa / Kristina Lakomek / Mike Strauss / Manuela Moldt / Karl-Peter Hopfner
DateDeposition: Jan 31, 2018 / Header (metadata) release: Mar 14, 2018 / Map release: Apr 25, 2018 / Last update: Apr 25, 2018

Structure visualization

  • Surface view with section colored by density value
  • Surface level: 0.023
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.023
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
Supplemental images

Downloads & links


Fileemd_4278.map.gz (map file in CCP4 format, 157217 KB)
Projections & slices

Image control

AxesZ (Sec.)Y (Row.)X (Col.)
340 pix
1.06 Å/pix.
= 360.4 Å
340 pix
1.06 Å/pix.
= 360.4 Å
340 pix
1.06 Å/pix.
= 360.4 Å



Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Contour Level:0.023 (by author), 0.023 (movie #1):
Minimum - Maximum-0.06688581 - 0.12919313
Average (Standard dev.)-0.00009406648 (0.0046275714)


Space Group Number1
Map Geometry
Axis orderXYZ
CellA=B=C: 360.4 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.061.061.06
M x/y/z340340340
origin x/y/z0.0000.0000.000
length x/y/z360.400360.400360.400
start NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
D min/max/mean-0.0670.129-0.000

Supplemental data

Sample components

Entire INO80core Nucleosome complex

EntireName: INO80core Nucleosome complex / Number of components: 1

Component #1: protein, INO80core Nucleosome complex

ProteinName: INO80core Nucleosome complex / Recombinant expression: No
MassTheoretical: 1000 kDa
SourceSpecies: Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
Source (engineered)Expression System: Trichoplusia ni (cabbage looper)

Experimental details

Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionSpecimen conc.: 1 mg/ml
Buffer solution: 20 mM HEPES pH 8, 60 mM KCl, 0.5% glycerol, 0.25 mM CaCl2, 20 uM ZnCl2, 0.25 mM DTT, 0.05% Octyl-beta-glucoside
pH: 8
VitrificationInstrument: LEICA EM GP / Cryogen name: ETHANE / Temperature: 281 K / Humidity: 95 %

Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 59.6 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD / Defocus: - 3500.0 nm
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

Image acquisition

Image acquisitionNumber of digital images: 3992
Details: Images were collected in movie mode with 4 frames per second and 10s total aquisition

Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 16287
3D reconstructionSoftware: RELION / Resolution: 4.68 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot
(resolution estimation)

About Yorodumi


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. (see PDBe EMDB page)
  • 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 at EBI / 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. See below links for details.
  • 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

Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi

Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi

Read more


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.

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