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Yorodumi- EMDB-15996: Early transcription elongation state of influenza B/Mem polymeras... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-15996 | |||||||||
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Title | Early transcription elongation state of influenza B/Mem polymerase backtracked due to double incoproation of nucleotide analogue T1106 and with singly incoporated T1106 at the C +1 position | |||||||||
Map data | Loc-Scale filtered | |||||||||
Sample |
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Function / homology | Function and homology information symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / cap snatching / 7-methylguanosine mRNA capping / viral transcription / host cell mitochondrion / virion component / endonuclease activity / host cell cytoplasm / Hydrolases; Acting on ester bonds / RNA-directed RNA polymerase ...symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / cap snatching / 7-methylguanosine mRNA capping / viral transcription / host cell mitochondrion / virion component / endonuclease activity / host cell cytoplasm / Hydrolases; Acting on ester bonds / RNA-directed RNA polymerase / viral RNA genome replication / RNA-dependent RNA polymerase activity / nucleotide binding / DNA-templated transcription / host cell nucleus / RNA binding / metal ion binding Similarity search - Function | |||||||||
Biological species | Influenza B virus (B/Memphis/13/2003) / Influenza B virus | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.34 Å | |||||||||
Authors | Cusack S / Kouba T | |||||||||
Funding support | France, 1 items
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Citation | Journal: Cell Rep / Year: 2023 Title: Direct observation of backtracking by influenza A and B polymerases upon consecutive incorporation of the nucleoside analog T1106. Authors: Tomas Kouba / Anna Dubankova / Petra Drncova / Elisa Donati / Pietro Vidossich / Valentina Speranzini / Alex Pflug / Johanna Huchting / Chris Meier / Marco De Vivo / Stephen Cusack / Abstract: The antiviral pseudo-base T705 and its de-fluoro analog T1106 mimic adenine or guanine and can be competitively incorporated into nascent RNA by viral RNA-dependent RNA polymerases. Although ...The antiviral pseudo-base T705 and its de-fluoro analog T1106 mimic adenine or guanine and can be competitively incorporated into nascent RNA by viral RNA-dependent RNA polymerases. Although dispersed, single pseudo-base incorporation is mutagenic, consecutive incorporation causes polymerase stalling and chain termination. Using a template encoding single and then consecutive T1106 incorporation four nucleotides later, we obtained a cryogenic electron microscopy structure of stalled influenza A/H7N9 polymerase. This shows that the entire product-template duplex backtracks by 5 nt, bringing the singly incorporated T1106 to the +1 position, where it forms an unexpected T1106:U wobble base pair. Similar structures show that influenza B polymerase also backtracks after consecutive T1106 incorporation, regardless of whether prior single incorporation has occurred. These results give insight into the unusual mechanism of chain termination by pyrazinecarboxamide base analogs. Consecutive incorporation destabilizes the proximal end of the product-template duplex, promoting irreversible backtracking to a more energetically favorable overall configuration. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_15996.map.gz | 138.8 MB | EMDB map data format | |
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Header (meta data) | emd-15996-v30.xml emd-15996.xml | 23.6 KB 23.6 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_15996_fsc.xml | 14.8 KB | Display | FSC data file |
Images | emd_15996.png | 140.3 KB | ||
Others | emd_15996_additional_1.map.gz emd_15996_half_map_1.map.gz emd_15996_half_map_2.map.gz | 263.9 MB 225.1 MB 224.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-15996 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-15996 | HTTPS FTP |
-Related structure data
Related structure data | 8be0MC 7qtlC 7r0eC 7r1fC 7zplC 7zpmC 8bdrC 8bekC 8bf5C 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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-Map
File | Download / File: emd_15996.map.gz / Format: CCP4 / Size: 282.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | Loc-Scale filtered | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.645 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: Relion post-processed
File | emd_15996_additional_1.map | ||||||||||||
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Annotation | Relion post-processed | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half-map
File | emd_15996_half_map_1.map | ||||||||||||
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Annotation | Half-map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half-map
File | emd_15996_half_map_2.map | ||||||||||||
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Annotation | Half-map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Early transcription elongation state of influenza B/Mem polymeras...
+Supramolecule #1: Early transcription elongation state of influenza B/Mem polymeras...
+Macromolecule #1: Polymerase acidic protein
+Macromolecule #2: RNA-directed RNA polymerase catalytic subunit
+Macromolecule #3: Polymerase basic protein 2
+Macromolecule #4: 5' vRNA
+Macromolecule #5: 3' vRNA
+Macromolecule #6: mRNA
+Macromolecule #7: MAGNESIUM ION
+Macromolecule #8: P1-7-METHYLGUANOSINE-P3-ADENOSINE-5',5'-TRIPHOSPHATE
+Macromolecule #9: water
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 40.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |