+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-35905 | ||||||||||||||||||
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Title | The global structure of pre50S related to DbpA in state2 | ||||||||||||||||||
Map data | |||||||||||||||||||
Sample |
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Keywords | Ribosome / Biogenesis / pre50S / DbpA | ||||||||||||||||||
Biological species | Escherichia coli (E. coli) | ||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.92 Å | ||||||||||||||||||
Authors | Yu T / Zeng F | ||||||||||||||||||
Funding support | China, 5 items
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Citation | Journal: To Be Published Title: PTC Remodeling in Pre50S Intermediates: Insights into the Role of DEAD-box RNA Helicase DbpA Authors: Yu T / Jiang J / Yu Q / Li X / Dong W / Zeng F | ||||||||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_35905.map.gz | 202.6 MB | EMDB map data format | |
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Header (meta data) | emd-35905-v30.xml emd-35905.xml | 13.6 KB 13.6 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_35905_fsc.xml | 13.5 KB | Display | FSC data file |
Images | emd_35905.png | 137 KB | ||
Filedesc metadata | emd-35905.cif.gz | 4 KB | ||
Others | emd_35905_half_map_1.map.gz emd_35905_half_map_2.map.gz | 202.3 MB 202.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-35905 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-35905 | HTTPS FTP |
-Validation report
Summary document | emd_35905_validation.pdf.gz | 1.2 MB | Display | EMDB validaton report |
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Full document | emd_35905_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | emd_35905_validation.xml.gz | 21 KB | Display | |
Data in CIF | emd_35905_validation.cif.gz | 27.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-35905 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-35905 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_35905.map.gz / Format: CCP4 / Size: 216 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: 1.05 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #1
File | emd_35905_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_35905_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Ribosomal 50S subunit
Entire | Name: Ribosomal 50S subunit |
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Components |
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-Supramolecule #1: Ribosomal 50S subunit
Supramolecule | Name: Ribosomal 50S subunit / type: complex / ID: 1 / Parent: 0 / Details: Sample was purified by polysome profiling |
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Source (natural) | Organism: Escherichia coli (E. coli) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 Details: 25mM HEPES-KOH,pH7.5; 140mM NH4Cl; 10mM Mg2+; 1mM DTT |
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Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 4 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK II |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 30.0 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: 1.5 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |