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Yorodumi- EMDB-24765: Cryo-EM map of the phage AR9 non-virion RNA polymerase holoenzyme -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-24765 | |||||||||
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Title | Cryo-EM map of the phage AR9 non-virion RNA polymerase holoenzyme | |||||||||
Map data | Cryo-EM map of the phage AR9 non-virion RNA polymerase holoenzyme | |||||||||
Sample |
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Function / homology | Function and homology information RNA polymerase II activity / DNA-directed RNA polymerase complex / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / DNA-templated transcription / DNA binding / metal ion binding Similarity search - Function | |||||||||
Biological species | Bacillus phage AR9 (virus) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.1 Å | |||||||||
Authors | Fraser A / Leiman PG / Sokolova ML | |||||||||
Funding support | 1 items
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Citation | Journal: Nat Commun / Year: 2022 Title: Structural basis of template strand deoxyuridine promoter recognition by a viral RNA polymerase. Authors: Alec Fraser / Maria L Sokolova / Arina V Drobysheva / Julia V Gordeeva / Sergei Borukhov / John Jumper / Konstantin V Severinov / Petr G Leiman / Abstract: Recognition of promoters in bacterial RNA polymerases (RNAPs) is controlled by sigma subunits. The key sequence motif recognized by the sigma, the -10 promoter element, is located in the non-template ...Recognition of promoters in bacterial RNA polymerases (RNAPs) is controlled by sigma subunits. The key sequence motif recognized by the sigma, the -10 promoter element, is located in the non-template strand of the double-stranded DNA molecule ~10 nucleotides upstream of the transcription start site. Here, we explain the mechanism by which the phage AR9 non-virion RNAP (nvRNAP), a bacterial RNAP homolog, recognizes the -10 element of its deoxyuridine-containing promoter in the template strand. The AR9 sigma-like subunit, the nvRNAP enzyme core, and the template strand together form two nucleotide base-accepting pockets whose shapes dictate the requirement for the conserved deoxyuridines. A single amino acid substitution in the AR9 sigma-like subunit allows one of these pockets to accept a thymine thus expanding the promoter consensus. Our work demonstrates the extent to which viruses can evolve host-derived multisubunit enzymes to make transcription of their own genes independent of the host. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_24765.map.gz | 28.1 MB | EMDB map data format | |
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Header (meta data) | emd-24765-v30.xml emd-24765.xml | 12.3 KB 12.3 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_24765_fsc.xml | 7.2 KB | Display | FSC data file |
Images | emd_24765.png | 114.8 KB | ||
Others | emd_24765_half_map_1.map.gz emd_24765_half_map_2.map.gz | 22.9 MB 22.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-24765 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-24765 | HTTPS FTP |
-Validation report
Summary document | emd_24765_validation.pdf.gz | 651.5 KB | Display | EMDB validaton report |
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Full document | emd_24765_full_validation.pdf.gz | 651.1 KB | Display | |
Data in XML | emd_24765_validation.xml.gz | 13.1 KB | Display | |
Data in CIF | emd_24765_validation.cif.gz | 17.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-24765 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-24765 | HTTPS FTP |
-Related structure data
Related structure data | 7um1MC 7s00C 7s01C 7um0C 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_24765.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | Cryo-EM map of the phage AR9 non-virion RNA polymerase holoenzyme | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.08 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: Half map A
File | emd_24765_half_map_1.map | ||||||||||||
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Annotation | Half map A | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map B
File | emd_24765_half_map_2.map | ||||||||||||
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Annotation | Half map B | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Bacteriophage AR9 non-virion RNA polymerase holoenzyme
Entire | Name: Bacteriophage AR9 non-virion RNA polymerase holoenzyme |
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Components |
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-Supramolecule #1: Bacteriophage AR9 non-virion RNA polymerase holoenzyme
Supramolecule | Name: Bacteriophage AR9 non-virion RNA polymerase holoenzyme type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Bacillus phage AR9 (virus) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 20 mg/mL |
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Buffer | pH: 6.8 |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 43.2 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: 4.0 µm / Nominal defocus min: 1.0 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |