+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-15881 | |||||||||
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Title | NuA4 Histone Acetyltransferase Complex Full length Epl1 Core | |||||||||
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Sample |
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Keywords | NuA4 / histone acetyltransferase complex / Epigenetics / DNA repair / TRANSCRIPTION | |||||||||
Biological species | Komagataella phaffii GS115 (fungus) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.8 Å | |||||||||
Authors | Frechard A / Hexnerova R / Crucifix C / Papai G / Smirnova E / Faux C / Lo Ying Ping F / Helmlinger D / Schultz P / Ben-shem A | |||||||||
Funding support | France, 1 items
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Citation | Journal: Nat Struct Mol Biol / Year: 2023 Title: The structure of the NuA4-Tip60 complex reveals the mechanism and importance of long-range chromatin modification. Authors: Alexander Fréchard / Céline Faux / Rozalie Hexnerova / Corinne Crucifix / Gabor Papai / Ekaterina Smirnova / Conor McKeon / Florie Lo Ying Ping / Dominique Helmlinger / Patrick Schultz / Adam Ben-Shem / Abstract: Histone acetylation regulates most DNA transactions and is dynamically controlled by highly conserved enzymes. The only essential histone acetyltransferase (HAT) in yeast, Esa1, is part of the 1-MDa ...Histone acetylation regulates most DNA transactions and is dynamically controlled by highly conserved enzymes. The only essential histone acetyltransferase (HAT) in yeast, Esa1, is part of the 1-MDa NuA4 complex, which plays pivotal roles in both transcription and DNA-damage repair. NuA4 has the unique capacity to acetylate histone targets located several nucleosomes away from its recruitment site. Neither the molecular mechanism of this activity nor its physiological importance are known. Here we report the structure of the Pichia pastoris NuA4 complex, with its core resolved at 3.4-Å resolution. Three subunits, Epl1, Eaf1 and Swc4, intertwine to form a stable platform that coordinates all other modules. The HAT module is firmly anchored into the core while retaining the ability to stretch out over a long distance. We provide structural, biochemical and genetic evidence that an unfolded linker region of the Epl1 subunit is critical for this long-range activity. Specifically, shortening the Epl1 linker causes severe growth defects and reduced H4 acetylation levels over broad chromatin regions in fission yeast. Our work lays the foundations for a mechanistic understanding of NuA4's regulatory role and elucidates how its essential long-range activity is attained. #1: Journal: Res Sq / Year: 2022 Title: The structure of the NuA4/Tip60 complex reveals the mechanism and importance of long-range chromatin modification Authors: Schultz P / Frechard A / Hexnerova R / Crucifix C / Papai G / Smirnova E / Faux C / Ping F / Helmlinger D / Ben-Shem A | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_15881.map.gz | 5.2 MB | EMDB map data format | |
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Header (meta data) | emd-15881-v30.xml emd-15881.xml | 17.7 KB 17.7 KB | Display Display | EMDB header |
Images | emd_15881.png | 48 KB | ||
Masks | emd_15881_msk_1.map | 216 MB | Mask map | |
Others | emd_15881_half_map_1.map.gz emd_15881_half_map_2.map.gz | 200.3 MB 200.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-15881 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-15881 | HTTPS FTP |
-Validation report
Summary document | emd_15881_validation.pdf.gz | 1 MB | Display | EMDB validaton report |
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Full document | emd_15881_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | emd_15881_validation.xml.gz | 15.7 KB | Display | |
Data in CIF | emd_15881_validation.cif.gz | 18.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-15881 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-15881 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_15881.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.09 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_15881_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: Half map A
File | emd_15881_half_map_1.map | ||||||||||||
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Annotation | Half map A | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map B
File | emd_15881_half_map_2.map | ||||||||||||
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Annotation | Half map B | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : NuA4 histone acetyltransferase complex
Entire | Name: NuA4 histone acetyltransferase complex |
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Components |
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-Supramolecule #1: NuA4 histone acetyltransferase complex
Supramolecule | Name: NuA4 histone acetyltransferase complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6 |
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Source (natural) | Organism: Komagataella phaffii GS115 (fungus) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.25 mg/mL | |||||||||||||||||||||
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Buffer | pH: 8 Component:
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Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 279 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | TFS KRIOS |
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Specialist optics | Energy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 52.8 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.8000000000000003 µm / Nominal defocus min: 1.4000000000000001 µm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |