+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-35939 | ||||||||||||||||||
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Title | The global structure of pre50S related to DbpA in state3 | ||||||||||||||||||
Map data | |||||||||||||||||||
Sample |
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Keywords | Ribosome / pre50S / DbpA | ||||||||||||||||||
Function / homology | Function and homology information transcriptional attenuation / endoribonuclease inhibitor activity / RNA-binding transcription regulator activity / positive regulation of ribosome biogenesis / negative regulation of cytoplasmic translation / DnaA-L2 complex / translation repressor activity / negative regulation of DNA-templated DNA replication initiation / mRNA regulatory element binding translation repressor activity / ribosome assembly ...transcriptional attenuation / endoribonuclease inhibitor activity / RNA-binding transcription regulator activity / positive regulation of ribosome biogenesis / negative regulation of cytoplasmic translation / DnaA-L2 complex / translation repressor activity / negative regulation of DNA-templated DNA replication initiation / mRNA regulatory element binding translation repressor activity / ribosome assembly / assembly of large subunit precursor of preribosome / cytosolic ribosome assembly / response to reactive oxygen species / regulation of cell growth / DNA-templated transcription termination / response to radiation / mRNA 5'-UTR binding / large ribosomal subunit / ribosome binding / ribosomal large subunit assembly / transferase activity / large ribosomal subunit rRNA binding / 5S rRNA binding / cytoplasmic translation / cytosolic large ribosomal subunit / tRNA binding / negative regulation of translation / rRNA binding / ribosome / structural constituent of ribosome / translation / response to antibiotic / negative regulation of DNA-templated transcription / mRNA binding / DNA binding / RNA binding / zinc ion binding / cytosol / cytoplasm Similarity search - Function | ||||||||||||||||||
Biological species | Escherichia coli (E. coli) | ||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.6 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_35939.map.gz | 24.1 MB | EMDB map data format | |
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Header (meta data) | emd-35939-v30.xml emd-35939.xml | 42.9 KB 42.9 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_35939_fsc.xml | 13.5 KB | Display | FSC data file |
Images | emd_35939.png | 130.7 KB | ||
Filedesc metadata | emd-35939.cif.gz | 9.6 KB | ||
Others | emd_35939_half_map_1.map.gz emd_35939_half_map_2.map.gz | 202.6 MB 202.6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-35939 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-35939 | HTTPS FTP |
-Validation report
Summary document | emd_35939_validation.pdf.gz | 896 KB | Display | EMDB validaton report |
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Full document | emd_35939_full_validation.pdf.gz | 895.7 KB | Display | |
Data in XML | emd_35939_validation.xml.gz | 21.1 KB | Display | |
Data in CIF | emd_35939_validation.cif.gz | 27.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-35939 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-35939 | HTTPS FTP |
-Related structure data
Related structure data | 8j1zMC C: citing same article (ref.) M: atomic model generated by this map |
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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_35939.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: #2
File | emd_35939_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_35939_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Ribosome 50S subunit
+Supramolecule #1: Ribosome 50S subunit
+Macromolecule #1: 23S rRNA
+Macromolecule #2: 5S rRNA
+Macromolecule #3: 50S ribosomal protein L2
+Macromolecule #4: 50S ribosomal protein L3
+Macromolecule #5: 50S ribosomal protein L4
+Macromolecule #6: 50S ribosomal protein L5
+Macromolecule #7: 50S ribosomal protein L13
+Macromolecule #8: 50S ribosomal protein L14
+Macromolecule #9: 50S ribosomal protein L15
+Macromolecule #10: 50S ribosomal protein L17
+Macromolecule #11: 50S ribosomal protein L18
+Macromolecule #12: 50S ribosomal protein L19
+Macromolecule #13: 50S ribosomal protein L20
+Macromolecule #14: 50S ribosomal protein L21
+Macromolecule #15: 50S ribosomal protein L22
+Macromolecule #16: 50S ribosomal protein L23
+Macromolecule #17: 50S ribosomal protein L24
+Macromolecule #18: 50S ribosomal protein L25
+Macromolecule #19: 50S ribosomal protein L27
+Macromolecule #20: 50S ribosomal protein L28
+Macromolecule #21: 50S ribosomal protein L29
+Macromolecule #22: 50S ribosomal protein L30
+Macromolecule #23: 50S ribosomal protein L32
+Macromolecule #24: 50S ribosomal protein L33
+Macromolecule #25: 50S ribosomal protein L34
+Macromolecule #26: 50S ribosomal protein L35
+Macromolecule #27: 50S ribosomal protein L9
+Macromolecule #28: MAGNESIUM ION
+Macromolecule #29: water
-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: 20mM 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 / 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: DARK FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |