+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-4277 | ||||||||||||
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Title | CryoEM Structure INO80core Nucleosome complex | ||||||||||||
Map data | |||||||||||||
Sample |
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Function / homology | Function and homology information RMTs methylate histone arginines / DASH complex / heterochromatin formation => GO:0031507 / protein transport along microtubule to mitotic spindle pole body / mitotic sister chromatid biorientation / Metalloprotease DUBs / UCH proteinases / Ub-specific processing proteases / attachment of spindle microtubules to kinetochore / chromatin => GO:0000785 ...RMTs methylate histone arginines / DASH complex / heterochromatin formation => GO:0031507 / protein transport along microtubule to mitotic spindle pole body / mitotic sister chromatid biorientation / Metalloprotease DUBs / UCH proteinases / Ub-specific processing proteases / attachment of spindle microtubules to kinetochore / chromatin => GO:0000785 / Ino80 complex / attachment of mitotic spindle microtubules to kinetochore / negative regulation of megakaryocyte differentiation / ATP-dependent activity, acting on DNA / protein localization to CENP-A containing chromatin / Chromatin modifying enzymes / Replacement of protamines by nucleosomes in the male pronucleus / CENP-A containing nucleosome / Packaging Of Telomere Ends / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / Deposition of new CENPA-containing nucleosomes at the centromere / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / Inhibition of DNA recombination at telomere / Meiotic synapsis / telomere organization / RNA Polymerase I Promoter Opening / Interleukin-7 signaling / SUMOylation of chromatin organization proteins / Assembly of the ORC complex at the origin of replication / DNA methylation / Condensation of Prophase Chromosomes / HCMV Late Events / Chromatin modifications during the maternal to zygotic transition (MZT) / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / SIRT1 negatively regulates rRNA expression / innate immune response in mucosa / PRC2 methylates histones and DNA / helicase activity / Defective pyroptosis / HDACs deacetylate histones / RNA Polymerase I Promoter Escape / Nonhomologous End-Joining (NHEJ) / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / NoRC negatively regulates rRNA expression / G2/M DNA damage checkpoint / B-WICH complex positively regulates rRNA expression / HDMs demethylate histones / DNA Damage/Telomere Stress Induced Senescence / Metalloprotease DUBs / mitotic spindle / kinetochore / PKMTs methylate histone lysines / RMTs methylate histone arginines / Meiotic recombination / Pre-NOTCH Transcription and Translation / nucleosome assembly / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / UCH proteinases / nucleosome / antimicrobial humoral immune response mediated by antimicrobial peptide / E3 ubiquitin ligases ubiquitinate target proteins / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / RUNX1 regulates transcription of genes involved in differentiation of HSCs / chromatin organization / Factors involved in megakaryocyte development and platelet production / Processing of DNA double-strand break ends / HATs acetylate histones / antibacterial humoral response / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / DNA helicase / Estrogen-dependent gene expression / chromosome, telomeric region / Ub-specific processing proteases / defense response to Gram-positive bacterium / chromatin remodeling / Amyloid fiber formation / protein heterodimerization activity / DNA repair / enzyme binding / ATP hydrolysis activity / protein-containing complex / DNA binding / extracellular space / RNA binding / extracellular exosome / extracellular region / nucleoplasm / ATP binding / membrane / identical protein binding / nucleus Similarity search - Function | ||||||||||||
Biological species | Chaetomium thermophilum var. thermophilum DSM 1495 (fungus) / Homo sapiens (human) / synthetic construct (others) / Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.34 Å | ||||||||||||
Authors | Eustermann S / Schall K / Kostrewa D / Strauss M / Hopfner K | ||||||||||||
Funding support | Germany, 3 items
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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 / Abstract: In the eukaryotic nucleus, DNA is packaged in the form of nucleosomes, each of which comprises about 147 base pairs of DNA wrapped around a histone protein octamer. The position and histone ...In the eukaryotic nucleus, DNA is packaged in the form of nucleosomes, each of which comprises about 147 base pairs of DNA wrapped around a histone protein octamer. The position and histone composition of nucleosomes is governed by ATP-dependent chromatin remodellers such as the 15-subunit INO80 complex . INO80 regulates gene expression, DNA repair and replication by sliding nucleosomes, the exchange of histone H2A.Z with H2A, and the positioning of + 1 and -1 nucleosomes at promoter DNA. The structures and mechanisms of these remodelling reactions are currently unknown. Here we report the cryo-electron microscopy structure of the evolutionarily conserved core of the INO80 complex from the fungus Chaetomium thermophilum bound to a nucleosome, at a global resolution of 4.3 Å and with major parts at 3.7 Å. The INO80 core cradles one entire gyre of the nucleosome through multivalent DNA and histone contacts. An Rvb1/Rvb2 AAA ATPase heterohexamer is an assembly scaffold for the complex and acts as a 'stator' for the motor and nucleosome-gripping subunits. The Swi2/Snf2 ATPase motor binds to nucleosomal DNA at superhelical location -6, unwraps approximately 15 base pairs, disrupts the H2A-DNA contacts and is poised to pump entry DNA into the nucleosome. Arp5 and Ies6 bind superhelical locations -2 and -3 to act as a counter grip for the motor, on the other side of the H2A-H2B dimer. The Arp5 insertion domain forms a grappler element that binds the nucleosome dyad, connects the Arp5 actin-fold and entry DNA over a distance of about 90 Å and packs against histone H2A-H2B near the 'acidic patch'. Our structure together with biochemical data suggests a unified mechanism for nucleosome sliding and histone editing by INO80. The motor is part of a macromolecular ratchet, persistently pumping entry DNA across the H2A-H2B dimer against the Arp5 grip until a large nucleosome translocation step occurs. The transient exposure of H2A-H2B by motor activity as well as differential recognition of H2A.Z and H2A may regulate histone exchange. | ||||||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_4277.map.gz | 88.4 MB | EMDB map data format | |
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Header (meta data) | emd-4277-v30.xml emd-4277.xml | 34.8 KB 34.8 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_4277_fsc.xml | 12.2 KB | Display | FSC data file |
Images | emd_4277.png | 63 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-4277 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-4277 | HTTPS FTP |
-Related structure data
Related structure data | 6fmlMC 4264C 4278C 4280C 6fhsC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_4277.map.gz / Format: CCP4 / Size: 149.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 1.06 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
+Entire : INO80core Nucleosome Complex
+Supramolecule #1: INO80core Nucleosome Complex
+Supramolecule #2: INO80core
+Supramolecule #3: Histone octamer
+Supramolecule #4: Synthetic deoxyribonucleic acid
+Macromolecule #1: RuvB-like helicase
+Macromolecule #2: RuvB-like helicase
+Macromolecule #3: Ino80
+Macromolecule #4: les2
+Macromolecule #5: Ies6
+Macromolecule #6: Actin related protein 5
+Macromolecule #9: Histone H3.2
+Macromolecule #10: Histone H4
+Macromolecule #11: Histone H2A type 1
+Macromolecule #12: Histone H2B type 1-C/E/F/G/I
+Macromolecule #7: Nucleosomal DNA Strand 1
+Macromolecule #8: Nucleosomal DNA Strand 2
+Macromolecule #13: ADENOSINE-5'-DIPHOSPHATE
+Macromolecule #14: ADENOSINE-5'-TRIPHOSPHATE
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1 mg/mL |
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Buffer | pH: 8 Details: 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 |
Grid | Model: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 281 K / Instrument: LEICA EM GP |
Details | Monodisperse sample: INO80core complex reconstituted with nucleosomal substrate was purified by gelfiltration. Addition of nucleotides or crosslinking was not required. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated defocus min: 1.3 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 3.5 µm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Frames/image: 1-40 / Number grids imaged: 1 / Number real images: 3992 / Average electron dose: 59.6 e/Å2 Details: Images were collected in movie mode with 4 frames per second and 10s total aquisition |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |