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Yorodumi- EMDB-15709: Structure of a nucleosome-bound MuvB transcription factor complex... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-15709 | |||||||||
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Title | Structure of a nucleosome-bound MuvB transcription factor complex reveals DNA remodelling | |||||||||
Map data | MMBcore:NCP overall refined map at 10 Angstrom resolution | |||||||||
Sample |
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Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 10.0 Å | |||||||||
Authors | Alfieri C | |||||||||
Funding support | United Kingdom, 1 items
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Citation | Journal: Nat Commun / Year: 2022 Title: Structure of a nucleosome-bound MuvB transcription factor complex reveals DNA remodelling. Authors: Marios G Koliopoulos / Reyhan Muhammad / Theodoros I Roumeliotis / Fabienne Beuron / Jyoti S Choudhary / Claudio Alfieri / Abstract: Genes encoding the core cell cycle machinery are transcriptionally regulated by the MuvB family of protein complexes in a cell cycle-specific manner. Complexes of MuvB with the transcription factors ...Genes encoding the core cell cycle machinery are transcriptionally regulated by the MuvB family of protein complexes in a cell cycle-specific manner. Complexes of MuvB with the transcription factors B-MYB and FOXM1 activate mitotic genes during cell proliferation. The mechanisms of transcriptional regulation by these complexes are still poorly characterised. Here, we combine biochemical analysis and in vitro reconstitution, with structural analysis by cryo-electron microscopy and cross-linking mass spectrometry, to functionally examine these complexes. We find that the MuvB:B-MYB complex binds and remodels nucleosomes, thereby exposing nucleosomal DNA. This remodelling activity is supported by B-MYB which directly binds the remodelled DNA. Given the remodelling activity on the nucleosome, we propose that the MuvB:B-MYB complex functions as a pioneer transcription factor complex. In this work, we rationalise prior biochemical and cellular studies and provide a molecular framework of interactions on a protein complex that is key for cell cycle regulation. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_15709.map.gz | 2.7 MB | EMDB map data format | |
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Header (meta data) | emd-15709-v30.xml emd-15709.xml | 26.9 KB 26.9 KB | Display Display | EMDB header |
Images | emd_15709.png | 33.9 KB | ||
Others | emd_15709_additional_1.map.gz emd_15709_additional_2.map.gz emd_15709_additional_3.map.gz emd_15709_additional_4.map.gz emd_15709_additional_5.map.gz emd_15709_additional_6.map.gz emd_15709_additional_7.map.gz emd_15709_half_map_1.map.gz emd_15709_half_map_2.map.gz | 156.7 KB 2.9 MB 178.5 KB 3 MB 93.7 KB 29.5 MB 142.8 KB 2.7 MB 2.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-15709 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-15709 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_15709.map.gz / Format: CCP4 / Size: 3.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | MMBcore:NCP overall refined map at 10 Angstrom resolution | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 3.4884 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: MMB:DNA local refined map at 7.5 Angstrom resolution, sharpened more
File | emd_15709_additional_1.map | ||||||||||||
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Annotation | MMB:DNA local refined map at 7.5 Angstrom resolution, sharpened more | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: MMB:DNA local refined map at 7.5 Angstrom resolution
File | emd_15709_additional_2.map | ||||||||||||
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Annotation | MMB:DNA local refined map at 7.5 Angstrom resolution | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: NCP147 local refined map at 6.9 Angstrom resolution
File | emd_15709_additional_3.map | ||||||||||||
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Annotation | NCP147 local refined map at 6.9 Angstrom resolution | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: LIN9CTD:NCP local refined map at 7.1 Angstrom resolution
File | emd_15709_additional_4.map | ||||||||||||
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Annotation | LIN9CTD:NCP local refined map at 7.1 Angstrom resolution | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: MMBhead local refined map at 7.5 Angstrom resolution
File | emd_15709_additional_5.map | ||||||||||||
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Annotation | MMBhead local refined map at 7.5 Angstrom resolution | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: NCP127 local refined map at 3.3 Angstrom resolution
File | emd_15709_additional_6.map | ||||||||||||
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Annotation | NCP127 local refined map at 3.3 Angstrom resolution | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: LIN9:52CC local refined map at 8.7 Angstrom resolution
File | emd_15709_additional_7.map | ||||||||||||
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Annotation | LIN9:52CC local refined map at 8.7 Angstrom resolution | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: MMBcore:NCP overall refined map at 10 Angstrom resolution
File | emd_15709_half_map_1.map | ||||||||||||
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Annotation | MMBcore:NCP overall refined map at 10 Angstrom resolution | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: MMBcore:NCP overall refined map at 10 Angstrom resolution
File | emd_15709_half_map_2.map | ||||||||||||
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Annotation | MMBcore:NCP overall refined map at 10 Angstrom resolution | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : MuvBcore:B-MYB complex with a 167bp nucleosome
Entire | Name: MuvBcore:B-MYB complex with a 167bp nucleosome |
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Components |
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-Supramolecule #1: MuvBcore:B-MYB complex with a 167bp nucleosome
Supramolecule | Name: MuvBcore:B-MYB complex with a 167bp nucleosome / type: complex / Chimera: Yes / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Trichoplusia ni (cabbage looper) |
Molecular weight | Theoretical: 400 kDa/nm |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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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 / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.6 µm |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 1.5 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Initial angle assignment | Type: ANGULAR RECONSTITUTION |
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Final angle assignment | Type: ANGULAR RECONSTITUTION |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 10.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 237061 |