+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-7313 | |||||||||
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Title | Structure of human PRC2-AEBP2 | |||||||||
Map data | Structure of human PRC2-AEBP2 | |||||||||
Sample |
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Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.6 Å | |||||||||
Authors | Poepsel S / Kasinath V / Nogales E | |||||||||
Citation | Journal: Nat Struct Mol Biol / Year: 2018 Title: Cryo-EM structures of PRC2 simultaneously engaged with two functionally distinct nucleosomes. Authors: Simon Poepsel / Vignesh Kasinath / Eva Nogales / Abstract: Epigenetic regulation is mediated by protein complexes that couple recognition of chromatin marks to activity or recruitment of chromatin-modifying enzymes. Polycomb repressive complex 2 (PRC2), a ...Epigenetic regulation is mediated by protein complexes that couple recognition of chromatin marks to activity or recruitment of chromatin-modifying enzymes. Polycomb repressive complex 2 (PRC2), a gene silencer that methylates lysine 27 of histone H3, is stimulated upon recognition of its own catalytic product and has been shown to be more active on dinucleosomes than H3 tails or single nucleosomes. These properties probably facilitate local H3K27me2/3 spreading, causing heterochromatin formation and gene repression. Here, cryo-EM reconstructions of human PRC2 bound to bifunctional dinucleosomes show how a single PRC2, via interactions with nucleosomal DNA, positions the H3 tails of the activating and substrate nucleosome to interact with the EED subunit and the SET domain of EZH2, respectively. We show how the geometry of the PRC2-DNA interactions allows PRC2 to accommodate varying lengths of the linker DNA between nucleosomes. Our structures illustrate how an epigenetic regulator engages with a complex chromatin substrate. | |||||||||
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_7313.map.gz | 10.6 MB | EMDB map data format | |
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Header (meta data) | emd-7313-v30.xml emd-7313.xml | 13.6 KB 13.6 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_7313_fsc.xml | 5.2 KB | Display | FSC data file |
Images | emd_7313.png | 48.2 KB | ||
Others | emd_7313_half_map_1.map.gz emd_7313_half_map_2.map.gz | 8.6 MB 8.6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-7313 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-7313 | HTTPS FTP |
-Related structure data
Related structure data | 7306C 7307C 7308C 7309C 7310C 7311C 7312C C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_7313.map.gz / Format: CCP4 / Size: 11.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Structure of human PRC2-AEBP2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.68 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Half map: Structure of human PRC2-AEBP2, half map #1
File | emd_7313_half_map_1.map | ||||||||||||
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Annotation | Structure of human PRC2-AEBP2, half map #1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Structure of human PRC2-AEBP2, half map #2
File | emd_7313_half_map_2.map | ||||||||||||
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Annotation | Structure of human PRC2-AEBP2, half map #2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Human Polycomb Repressive Complex 2 (PRC2) including the accessor...
Entire | Name: Human Polycomb Repressive Complex 2 (PRC2) including the accessory subunit AEBP2 |
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Components |
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-Supramolecule #1: Human Polycomb Repressive Complex 2 (PRC2) including the accessor...
Supramolecule | Name: Human Polycomb Repressive Complex 2 (PRC2) including the accessory subunit AEBP2 type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Trichoplusia ni (cabbage looper) |
-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: 7.9 |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 60.0 e/Å2 |