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Yorodumi- EMDB-10629: Cryo EM map of BS3 crosslinked CoREST complex (LSD1:RCOR1:HDAC1) ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-10629 | |||||||||
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Title | Cryo EM map of BS3 crosslinked CoREST complex (LSD1:RCOR1:HDAC1) - open form | |||||||||
Map data | ||||||||||
Sample |
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Keywords | CoREST / RCOR1 / HDAC1 / LSD1 / GENE REGULATION | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 21.5 Å | |||||||||
Authors | Song Y / Fairall L / Ragan TJ / Savva CG / Morone N / Schwabe JWR | |||||||||
Funding support | United Kingdom, 1 items
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Citation | Journal: Cell Rep / Year: 2020 Title: Mechanism of Crosstalk between the LSD1 Demethylase and HDAC1 Deacetylase in the CoREST Complex. Authors: Yun Song / Lisbeth Dagil / Louise Fairall / Naomi Robertson / Mingxuan Wu / T J Ragan / Christos G Savva / Almutasem Saleh / Nobuhiro Morone / Micha B A Kunze / Andrew G Jamieson / Philip A ...Authors: Yun Song / Lisbeth Dagil / Louise Fairall / Naomi Robertson / Mingxuan Wu / T J Ragan / Christos G Savva / Almutasem Saleh / Nobuhiro Morone / Micha B A Kunze / Andrew G Jamieson / Philip A Cole / D Flemming Hansen / John W R Schwabe / Abstract: The transcriptional corepressor complex CoREST is one of seven histone deacetylase complexes that regulate the genome through controlling chromatin acetylation. The CoREST complex is unique in ...The transcriptional corepressor complex CoREST is one of seven histone deacetylase complexes that regulate the genome through controlling chromatin acetylation. The CoREST complex is unique in containing both histone demethylase and deacetylase enzymes, LSD1 and HDAC1, held together by the RCOR1 scaffold protein. To date, it has been assumed that the enzymes function independently within the complex. Now, we report the assembly of the ternary complex. Using both structural and functional studies, we show that the activity of the two enzymes is closely coupled and that the complex can exist in at least two distinct states with different kinetics. Electron microscopy of the complex reveals a bi-lobed structure with LSD1 and HDAC1 enzymes at opposite ends of the complex. The structure of CoREST in complex with a nucleosome reveals a mode of chromatin engagement that contrasts with previous models. | |||||||||
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_10629.map.gz | 23.5 MB | EMDB map data format | |
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Header (meta data) | emd-10629-v30.xml emd-10629.xml | 17.3 KB 17.3 KB | Display Display | EMDB header |
Images | emd_10629.png | 32.2 KB | ||
Filedesc metadata | emd-10629.cif.gz | 4.7 KB | ||
Others | emd_10629_half_map_1.map.gz emd_10629_half_map_2.map.gz | 5.7 MB 5.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-10629 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-10629 | HTTPS FTP |
-Related structure data
Related structure data | 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_10629.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 1.4 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Half map: #2
File | emd_10629_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_10629_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Ternary complex of RCOR1 with the demethylase LSD1 and the deacet...
Entire | Name: Ternary complex of RCOR1 with the demethylase LSD1 and the deacetylase HDAC1 |
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Components |
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-Supramolecule #1: Ternary complex of RCOR1 with the demethylase LSD1 and the deacet...
Supramolecule | Name: Ternary complex of RCOR1 with the demethylase LSD1 and the deacetylase HDAC1 type: complex / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 210 KDa |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.03 mg/mL | |||||||||
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Buffer | pH: 7.5 Component:
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Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV Details: 30 sec waiting time before blotting. Blot time 4 sec, blot force 10.. | |||||||||
Details | Sample was crosslinked with 2mM BS3 at room temperature for 5 minutes |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 0.5 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 105000 |
Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Temperature | Min: 80.0 K |
Image recording | Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3838 pixel / Digitization - Dimensions - Height: 3710 pixel / Digitization - Frames/image: 1-36 / Number grids imaged: 1 / Number real images: 1885 / Average exposure time: 14.0 sec. / Average electron dose: 32.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Particle selection | Number selected: 164247 / Details: Particles picked using crYOLO |
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Startup model | Type of model: INSILICO MODEL / In silico model: Relion 3.0 Initial Model |
Initial angle assignment | Type: PROJECTION MATCHING / Software - Name: RELION (ver. 3) |
Final 3D classification | Number classes: 4 / Software - Name: RELION (ver. 3) |
Final angle assignment | Type: PROJECTION MATCHING / Software - Name: RELION (ver. 3) |
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 21.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3) / Number images used: 6825 |