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Yorodumi- EMDB-25406: Cryo-EM structure of pioneer factor Cbf1 bound to the nucleosome -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-25406 | ||||||||||||||||||||||||||||||
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Title | Cryo-EM structure of pioneer factor Cbf1 bound to the nucleosome | ||||||||||||||||||||||||||||||
Map data | main map from cryoSPARC refinement | ||||||||||||||||||||||||||||||
Sample |
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Function / homology | Function and homology information Cbf1-Met4-Met28 complex / regulation of sulfur metabolic process / Condensation of Prophase Chromosomes / centromeric DNA binding / replication fork protection complex / RMTs methylate histone arginines / postreplication repair / chromosome, centromeric region / chromosome segregation / kinetochore ...Cbf1-Met4-Met28 complex / regulation of sulfur metabolic process / Condensation of Prophase Chromosomes / centromeric DNA binding / replication fork protection complex / RMTs methylate histone arginines / postreplication repair / chromosome, centromeric region / chromosome segregation / kinetochore / DNA-binding transcription repressor activity, RNA polymerase II-specific / structural constituent of chromatin / nucleosome / chromatin organization / DNA-binding transcription activator activity, RNA polymerase II-specific / RNA polymerase II-specific DNA-binding transcription factor binding / protein dimerization activity / chromatin remodeling / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / protein heterodimerization activity / DNA repair / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / mitochondrion / DNA binding / nucleoplasm / nucleus Similarity search - Function | ||||||||||||||||||||||||||||||
Biological species | Xenopus laevis (African clawed frog) / Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) / synthetic construct (others) | ||||||||||||||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.2 Å | ||||||||||||||||||||||||||||||
Authors | Eek P / Tan S | ||||||||||||||||||||||||||||||
Funding support | United States, Estonia, 9 items
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Citation | Journal: Mol Cell / Year: 2023 Title: Basic helix-loop-helix pioneer factors interact with the histone octamer to invade nucleosomes and generate nucleosome-depleted regions. Authors: Benjamin T Donovan / Hengye Chen / Priit Eek / Zhiyuan Meng / Caroline Jipa / Song Tan / Lu Bai / Michael G Poirier / Abstract: Nucleosomes drastically limit transcription factor (TF) occupancy, while pioneer transcription factors (PFs) somehow circumvent this nucleosome barrier. In this study, we compare nucleosome binding ...Nucleosomes drastically limit transcription factor (TF) occupancy, while pioneer transcription factors (PFs) somehow circumvent this nucleosome barrier. In this study, we compare nucleosome binding of two conserved S. cerevisiae basic helix-loop-helix (bHLH) TFs, Cbf1 and Pho4. A cryo-EM structure of Cbf1 in complex with the nucleosome reveals that the Cbf1 HLH region can electrostatically interact with exposed histone residues within a partially unwrapped nucleosome. Single-molecule fluorescence studies show that the Cbf1 HLH region facilitates efficient nucleosome invasion by slowing its dissociation rate relative to DNA through interactions with histones, whereas the Pho4 HLH region does not. In vivo studies show that this enhanced binding provided by the Cbf1 HLH region enables nucleosome invasion and ensuing repositioning. These structural, single-molecule, and in vivo studies reveal the mechanistic basis of dissociation rate compensation by PFs and how this translates to facilitating chromatin opening inside cells. | ||||||||||||||||||||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_25406.map.gz | 17.8 MB | EMDB map data format | |
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Header (meta data) | emd-25406-v30.xml emd-25406.xml | 31.3 KB 31.3 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_25406_fsc.xml | 8.9 KB | Display | FSC data file |
Images | emd_25406.png | 120.7 KB | ||
Masks | emd_25406_msk_1.map emd_25406_msk_2.map | 64 MB 64 MB | Mask map | |
Others | emd_25406_additional_1.map.gz emd_25406_half_map_1.map.gz emd_25406_half_map_2.map.gz | 57.5 MB 59.5 MB 59.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-25406 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-25406 | HTTPS FTP |
-Related structure data
Related structure data | 7ssaMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_25406.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | main map from cryoSPARC refinement | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.288 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_25406_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Mask #2
File | emd_25406_msk_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: map postprocessed with deepEMhancer
File | emd_25406_additional_1.map | ||||||||||||
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Annotation | map postprocessed with deepEMhancer | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map A from cryoSPARC refinement
File | emd_25406_half_map_1.map | ||||||||||||
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Annotation | half map A from cryoSPARC refinement | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map B from cryoSPARC refinement
File | emd_25406_half_map_2.map | ||||||||||||
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Annotation | half map B from cryoSPARC refinement | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Pioneer factor Cbf1 in complex with the nucleosome
+Supramolecule #1: Pioneer factor Cbf1 in complex with the nucleosome
+Supramolecule #2: Histone H3.2, Histone H4
+Supramolecule #3: Histone H2A.1, Histone H2B.1
+Supramolecule #4: Centromere-binding protein 1
+Supramolecule #5: DNA
+Macromolecule #1: Histone H3.2
+Macromolecule #2: Histone H4
+Macromolecule #3: Histone H2A.1
+Macromolecule #4: Histone H2B.1
+Macromolecule #5: Centromere-binding protein 1
+Macromolecule #6: DNA (137-MER)
+Macromolecule #7: DNA (137-MER)
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1.0 mg/mL | |||||||||||||||
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Buffer | pH: 7.5 Component:
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Grid | Model: Quantifoil R1.2/1.3 / Pretreatment - Type: GLOW DISCHARGE | |||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | TFS 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 / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 18000 |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 6339 / Average electron dose: 50.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |