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- EMDB-24763: Cryo-EM map of the phage AR9 non-virion RNA polymerase holoenzyme... -
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Open data
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Basic information
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Title | Cryo-EM map of the phage AR9 non-virion RNA polymerase holoenzyme in complex with DNA containing the AR9 P077 promoter | |||||||||
![]() | Cryo-EM map of bacteriophage AR9 non-virion RNA polymerase in complex with two oligonucleotides containing two P077 promoters. | |||||||||
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Function / homology | ![]() DNA-directed RNA polymerase complex / RNA polymerase II activity / 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 | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.8 Å | |||||||||
![]() | Fraser A / Leiman PG / Sokolova ML | |||||||||
Funding support | 1 items
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![]() | ![]() 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 | ![]() | 28 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 12.8 KB 12.8 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 10.4 KB | Display | ![]() |
Images | ![]() | 109.8 KB | ||
Others | ![]() ![]() | 22.9 MB 22.9 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 730.6 KB | Display | ![]() |
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Full document | ![]() | 730.2 KB | Display | |
Data in XML | ![]() | 15.8 KB | Display | |
Data in CIF | ![]() | 20.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7um0MC ![]() 7s00C ![]() 7s01C ![]() 7um1C M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
File | ![]() | ||||||||||||||||||||
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Annotation | Cryo-EM map of bacteriophage AR9 non-virion RNA polymerase in complex with two oligonucleotides containing two P077 promoters. | ||||||||||||||||||||
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_24763_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_24763_half_map_2.map | ||||||||||||
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Annotation | Half map B | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : AR9 nvRNAP promoter complex
Entire | Name: AR9 nvRNAP promoter complex |
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Components |
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-Supramolecule #1: AR9 nvRNAP promoter complex
Supramolecule | Name: AR9 nvRNAP promoter complex / type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: #1 Details: The complex consists of the AR9 nvRNAP holoenzyme and two copies of the same oligonucleotide containing the P077 promoter. Only three bases in one of the oligonucleotides are sufficiently ...Details: The complex consists of the AR9 nvRNAP holoenzyme and two copies of the same oligonucleotide containing the P077 promoter. Only three bases in one of the oligonucleotides are sufficiently ordered for atomic model building. |
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Source (natural) | Organism: ![]() |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 10 mg/mL |
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Buffer | pH: 6.8 |
Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER |
Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 43.68 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
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 |