+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-4511 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Influenza B polymerase pre-initiation complex | |||||||||
Map data | Influenza virus B polymerase per-initiation complex (LocScale filtered) | |||||||||
Sample |
| |||||||||
Keywords | Influenza polzmerase / Viral protein | |||||||||
Function / homology | Function and homology information viral transcription / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / host cell mitochondrion / 7-methylguanosine mRNA capping / cap snatching / virion component / endonuclease activity / host cell cytoplasm / Hydrolases; Acting on ester bonds / RNA-directed RNA polymerase ...viral transcription / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / host cell mitochondrion / 7-methylguanosine mRNA capping / cap snatching / 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 / DNA-templated transcription / nucleotide binding / host cell nucleus / RNA binding / metal ion binding Similarity search - Function | |||||||||
Biological species | Influenza B virus | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.1 Å | |||||||||
Authors | Cusack S / Kouba T | |||||||||
Citation | Journal: Nat Struct Mol Biol / Year: 2019 Title: Structural snapshots of actively transcribing influenza polymerase. Authors: Tomas Kouba / Petra Drncová / Stephen Cusack / Abstract: Influenza virus RNA-dependent RNA polymerase uses unique mechanisms to transcribe its single-stranded genomic viral RNA (vRNA) into messenger RNA. The polymerase is initially bound to a promoter ...Influenza virus RNA-dependent RNA polymerase uses unique mechanisms to transcribe its single-stranded genomic viral RNA (vRNA) into messenger RNA. The polymerase is initially bound to a promoter comprising the partially base-paired 3' and 5' extremities of the RNA. A short, capped primer, 'cap-snatched' from a nascent host polymerase II transcript, is directed towards the polymerase active site to initiate RNA synthesis. Here we present structural snapshots, as determined by X-ray crystallography and cryo-electron microscopy, of actively initiating influenza polymerase as it transitions towards processive elongation. Unexpected conformational changes unblock the active site cavity to allow establishment of a nine-base-pair template-product RNA duplex before the strands separate into distinct exit channels. Concomitantly, as the template translocates, the promoter base pairs are broken and the template entry region is remodeled. These structures reveal details of the influenza polymerase active site that will help optimize nucleoside analogs or other compounds that directly inhibit viral RNA synthesis. | |||||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_4511.map.gz | 4.6 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-4511-v30.xml emd-4511.xml | 18.6 KB 18.6 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_4511_fsc.xml | 11.1 KB | Display | FSC data file |
Images | emd_4511.png | 72 KB | ||
Filedesc metadata | emd-4511.cif.gz | 7.2 KB | ||
Others | emd_4511_additional.map.gz | 108.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-4511 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-4511 | HTTPS FTP |
-Validation report
Summary document | emd_4511_validation.pdf.gz | 254.4 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_4511_full_validation.pdf.gz | 253.5 KB | Display | |
Data in XML | emd_4511_validation.xml.gz | 12.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4511 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4511 | HTTPS FTP |
-Related structure data
Related structure data | 6qcsMC 4512C 6qctC 6qcvC 6qcwC 6qcxC M: atomic model generated by this map C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|
-Map
File | Download / File: emd_4511.map.gz / Format: CCP4 / Size: 115.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Influenza virus B polymerase per-initiation complex (LocScale filtered) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.8311 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Additional map: Influenza virus B polymerase per-initiation complex (Relion post-process)...
File | emd_4511_additional.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Influenza virus B polymerase per-initiation complex (Relion post-process) | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Sample components
+Entire : Influenza polymerase pre-initiation complex
+Supramolecule #1: Influenza polymerase pre-initiation complex
+Supramolecule #2: Influenza polymerase pre-initiation complex
+Supramolecule #3: Influenza polymerase pre-initiation complex
+Macromolecule #1: Polymerase acidic protein
+Macromolecule #2: RNA-directed RNA polymerase catalytic subunit
+Macromolecule #3: Polymerase basic protein 2
+Macromolecule #4: Capped RNA
+Macromolecule #5: 5 end
+Macromolecule #6: 3 end
+Macromolecule #7: MAGNESIUM ION
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
---|---|
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Image recording | Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 22.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |