|Entry||Database: EMDB / ID: 4278|
|Title||CryoEM structure of INO80core Nucleosome complex in closed grappler conformation|
|Sample||INO80core Nucleosome complex:|
|Function / homology||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 ...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
|Source||Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)|
|Method||single particle reconstruction / cryo EM / 4.68 Å resolution|
|Authors||Eustermann S / Schall K / Strauss M / Hopnfer KP|
|Citation||Journal: 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
|Date||Deposition: Jan 31, 2018 / Header (metadata) release: Mar 14, 2018 / Map release: Apr 25, 2018 / Last update: Apr 25, 2018|
|Structure viewer||EM map: |
Downloads & links
|File||emd_4278.map.gz (map file in CCP4 format, 157217 KB)|
|Projections & slices|
Images are generated by Spider.
|Voxel size||X=Y=Z: 1.06 Å|
CCP4 map header:
-Entire INO80core Nucleosome complex
|Entire||Name: INO80core Nucleosome complex / Number of components: 1|
-Component #1: protein, INO80core Nucleosome complex
|Protein||Name: INO80core Nucleosome complex / Recombinant expression: No|
|Mass||Theoretical: 1000 kDa|
|Source||Species: Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)|
|Source (engineered)||Expression System: Trichoplusia ni (cabbage looper)|
|Specimen||Specimen state: particle / Method: cryo EM|
|Sample solution||Specimen 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
|Vitrification||Instrument: LEICA EM GP / Cryogen name: ETHANE / Temperature: 281 K / Humidity: 95 %|
-Electron microscopy imaging
Model: Titan Krios / Image courtesy: FEI Company
|Imaging||Microscope: FEI TITAN KRIOS|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 59.6 e/Å2 / Illumination mode: FLOOD BEAM|
|Lens||Imaging mode: BRIGHT FIELD / Defocus: - 3500.0 nm|
|Specimen Holder||Model: FEI TITAN KRIOS AUTOGRID HOLDER|
|Camera||Detector: GATAN K2 SUMMIT (4k x 4k)|
|Image acquisition||Number of digital images: 3992|
Details: Images were collected in movie mode with 4 frames per second and 10s total aquisition
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