+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-34206 | |||||||||
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Title | Cryo-EM structure of PRC1 bound to unmodified nucleosome | |||||||||
Map data | ||||||||||
Sample |
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Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.48 Å | |||||||||
Authors | Ai HS / Zebin T / Zhiheng D / Jiakun T / Liying Z / Jia-Bin L / Man P / Liu L | |||||||||
Funding support | China, 1 items
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Citation | Journal: Chem / Year: 2023 Title: Synthetic E2-Ub-nucleosome conjugates for studying nucleosome ubiquitination. Authors: Ai HS / Tong Z / Deng Z / Tian J / Zhang L / Sun M / Du Y / Xu Z / Shi Q / Liang L / Zheng Q / Li JB / Pan M / Liu L | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_34206.map.gz | 4.7 MB | EMDB map data format | |
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Header (meta data) | emd-34206-v30.xml emd-34206.xml | 12.1 KB 12.1 KB | Display Display | EMDB header |
Images | emd_34206.png | 97.2 KB | ||
Masks | emd_34206_msk_1.map | 64 MB | Mask map | |
Others | emd_34206_half_map_1.map.gz emd_34206_half_map_2.map.gz | 49.5 MB 49.6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-34206 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-34206 | HTTPS FTP |
-Validation report
Summary document | emd_34206_validation.pdf.gz | 598.9 KB | Display | EMDB validaton report |
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Full document | emd_34206_full_validation.pdf.gz | 598.5 KB | Display | |
Data in XML | emd_34206_validation.xml.gz | 12.1 KB | Display | |
Data in CIF | emd_34206_validation.cif.gz | 14.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-34206 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-34206 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_34206.map.gz / Format: CCP4 / Size: 64 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: 1.074 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_34206_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_34206_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_34206_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Complex of PRC1 and unmodified nucleosome
Entire | Name: Complex of PRC1 and unmodified nucleosome |
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Components |
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-Supramolecule #1: Complex of PRC1 and unmodified nucleosome
Supramolecule | Name: Complex of PRC1 and unmodified nucleosome / type: complex / ID: 1 / Chimera: Yes / Parent: 0 |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 230 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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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.48 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 25647 |
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Initial angle assignment | Type: ANGULAR RECONSTITUTION |
Final angle assignment | Type: ANGULAR RECONSTITUTION |