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Yorodumi- EMDB-17865: Tilapia Lake Virus polymerase in vRNA elongation state with addit... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-17865 | |||||||||
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Title | Tilapia Lake Virus polymerase in vRNA elongation state with additional mode B promoter (transcriptase conformation) | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Viral polymerase / VIRAL PROTEIN | |||||||||
Function / homology | RNA-dependent RNA polymerase activity / DNA/RNA polymerase superfamily / Uncharacterized protein / Putative PB1 / RNA-dependent RNA polymerase Function and homology information | |||||||||
Biological species | Tilapia lake virus | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.42 Å | |||||||||
Authors | Arragain B / Cusack S | |||||||||
Funding support | France, 1 items
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Citation | Journal: Nat Commun / Year: 2023 Title: Structural and functional analysis of the minimal orthomyxovirus-like polymerase of Tilapia Lake Virus from the highly diverged Amnoonviridae family. Authors: Benoit Arragain / Martin Pelosse / Albert Thompson / Stephen Cusack / Abstract: Tilapia Lake Virus (TiLV), a recently discovered pathogen of tilapia fish, belongs to the Amnoonviridae family from the Articulavirales order. Its ten genome segments have characteristic conserved ...Tilapia Lake Virus (TiLV), a recently discovered pathogen of tilapia fish, belongs to the Amnoonviridae family from the Articulavirales order. Its ten genome segments have characteristic conserved ends and encode proteins with no known homologues, apart from the segment 1, which encodes an orthomyxo-like RNA-dependent-RNA polymerase core subunit. Here we show that segments 1-3 encode respectively the PB1, PB2 and PA-like subunits of an active heterotrimeric polymerase that maintains all domains found in the distantly related influenza polymerase, despite an unprecedented overall size reduction of 40%. Multiple high-resolution cryo-EM structures of TiLV polymerase in pre-initiation, initiation and active elongation states, show how it binds the vRNA and cRNA promoters and performs RNA synthesis, with both transcriptase and replicase configurations being characterised. However, the highly truncated endonuclease-like domain appears inactive and the putative cap-binding domain is autoinhibited, emphasising that many functional aspects of TiLV polymerase remain to be elucidated. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_17865.map.gz | 9 MB | EMDB map data format | |
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Header (meta data) | emd-17865-v30.xml emd-17865.xml | 22.1 KB 22.1 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_17865_fsc.xml | 10.6 KB | Display | FSC data file |
Images | emd_17865.png | 87.1 KB | ||
Masks | emd_17865_msk_1.map | 103 MB | Mask map | |
Filedesc metadata | emd-17865.cif.gz | 7 KB | ||
Others | emd_17865_additional_1.map.gz emd_17865_half_map_1.map.gz emd_17865_half_map_2.map.gz | 80.9 MB 81.1 MB 80.8 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-17865 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-17865 | HTTPS FTP |
-Validation report
Summary document | emd_17865_validation.pdf.gz | 875.7 KB | Display | EMDB validaton report |
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Full document | emd_17865_full_validation.pdf.gz | 875.2 KB | Display | |
Data in XML | emd_17865_validation.xml.gz | 17.6 KB | Display | |
Data in CIF | emd_17865_validation.cif.gz | 22.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-17865 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-17865 | HTTPS FTP |
-Related structure data
Related structure data | 8pszMC 8psnC 8psoC 8psqC 8pssC 8psuC 8psxC 8pt2C 8pt6C 8pt7C 8pthC 8ptjC 8qz8C 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_17865.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 0.84 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_17865_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: #1
File | emd_17865_additional_1.map | ||||||||||||
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Density Histograms |
-Half map: #2
File | emd_17865_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_17865_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Tilapia lake virus polymerase
+Supramolecule #1: Tilapia lake virus polymerase
+Macromolecule #1: Polymerase acidic protein (PA-like)
+Macromolecule #2: Putative PB1
+Macromolecule #3: RNA-dependent RNA polymerase
+Macromolecule #4: 5' vRNA end - vRNA loop (40-mer)
+Macromolecule #5: Transcription-like product
+Macromolecule #6: ZINC ION
+Macromolecule #7: [(2~{R},3~{S},4~{R},5~{R})-5-(4-azanyl-2-oxidanylidene-pyrimidin-...
+Macromolecule #8: MAGNESIUM ION
+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: 8 |
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Vitrification | Cryogen name: ETHANE |
-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: 40.0 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: 2.0 µm / Nominal defocus min: 0.8 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: AB INITIO MODEL |
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Output model | PDB-8psz: |