+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-40691 | |||||||||
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Title | Focused classification of site c OCT4 | |||||||||
Map data | ||||||||||
Sample |
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Keywords | nucleosome / transcription factor / transcription / CHROMATIN BINDING PROTEIN-DNA complex / GENE REGULATION / GENE REGULATION-DNA complex / TRANSCRIPTION-DNA complex | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 7.9 Å | |||||||||
Authors | Tengfei L / Ruifang G / Yawen B | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Mol Cell / Year: 2023 Title: Structural mechanism of LIN28B nucleosome targeting by OCT4. Authors: Ruifang Guan / Tengfei Lian / Bing-Rui Zhou / David Wheeler / Yawen Bai / Abstract: Pioneer transcription factors are essential for cell fate changes by targeting closed chromatin. OCT4 is a crucial pioneer factor that can induce cell reprogramming. However, the structural basis of ...Pioneer transcription factors are essential for cell fate changes by targeting closed chromatin. OCT4 is a crucial pioneer factor that can induce cell reprogramming. However, the structural basis of how pioneer factors recognize the in vivo nucleosomal DNA targets is unknown. Here, we determine the high-resolution structures of the nucleosome containing human LIN28B DNA and its complexes with the OCT4 DNA binding region. Three OCT4s bind the pre-positioned nucleosome by recognizing non-canonical DNA sequences. Two use their POUS domains while the other uses the POUS-loop-POUHD region; POUHD serves as a wedge to unwrap ∼25 base pair DNA. Our analysis of previous genomic data and determination of the ESRRB-nucleosome-OCT4 structure confirmed the generality of these structural features. Moreover, biochemical studies suggest that multiple OCT4s cooperatively open the H1-condensed nucleosome array containing the LIN28B nucleosome. Thus, our study suggests a mechanism of how OCT4 can target the nucleosome and open closed chromatin. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_40691.map.gz | 544 KB | EMDB map data format | |
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Header (meta data) | emd-40691-v30.xml emd-40691.xml | 13.3 KB 13.3 KB | Display Display | EMDB header |
Images | emd_40691.png | 13.3 KB | ||
Others | emd_40691_half_map_1.map.gz emd_40691_half_map_2.map.gz | 24.7 MB 24.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-40691 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-40691 | HTTPS FTP |
-Validation report
Summary document | emd_40691_validation.pdf.gz | 445.5 KB | Display | EMDB validaton report |
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Full document | emd_40691_full_validation.pdf.gz | 445.1 KB | Display | |
Data in XML | emd_40691_validation.xml.gz | 11.7 KB | Display | |
Data in CIF | emd_40691_validation.cif.gz | 13.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-40691 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-40691 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_40691.map.gz / Format: CCP4 / Size: 52.7 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: 1.056 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #1
File | emd_40691_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_40691_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : focused classification of site C OCT4
Entire | Name: focused classification of site C OCT4 |
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Components |
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-Supramolecule #1: focused classification of site C OCT4
Supramolecule | Name: focused classification of site C OCT4 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#8 |
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Source (natural) | Organism: Homo sapiens (human) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.3 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 53.8 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: NONE |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 7.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 30272 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |