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Yorodumi- PDB-8z8n: Cryo-EM structure of Thogoto virus polymerase in transcription pr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8z8n | ||||||
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Title | Cryo-EM structure of Thogoto virus polymerase in transcription pre-initiation conformation 3 | ||||||
Components |
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Keywords | TRANSCRIPTION / RNA polymerase | ||||||
Function / homology | Function and homology information cap snatching / 7-methylguanosine mRNA capping / virion component / RNA-directed RNA polymerase / viral RNA genome replication / RNA-dependent RNA polymerase activity / nucleotide binding / host cell nucleus / RNA binding Similarity search - Function | ||||||
Biological species | Thogoto virus | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.79 Å | ||||||
Authors | Xue, L. / Chang, T. / Li, Z. / Zhao, H. / Li, M. / He, J. / Chen, X. / Xiong, X. | ||||||
Funding support | China, 1items
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Citation | Journal: Nat Commun / Year: 2024 Title: Cryo-EM structures of Thogoto virus polymerase reveal unique RNA transcription and replication mechanisms among orthomyxoviruses. Authors: Lu Xue / Tiancai Chang / Zimu Li / Chenchen Wang / Heyu Zhao / Mei Li / Peng Tang / Xin Wen / Mengmeng Yu / Jiqin Wu / Xichen Bao / Xiaojun Wang / Peng Gong / Jun He / Xinwen Chen / Xiaoli Xiong / Abstract: Influenza viruses and thogotoviruses account for most recognized orthomyxoviruses. Thogotoviruses, exemplified by Thogoto virus (THOV), are capable of infecting humans using ticks as vectors. THOV ...Influenza viruses and thogotoviruses account for most recognized orthomyxoviruses. Thogotoviruses, exemplified by Thogoto virus (THOV), are capable of infecting humans using ticks as vectors. THOV transcribes mRNA without the extraneous 5' end sequences derived from cap-snatching in influenza virus mRNA. Here, we report cryo-EM structures to characterize THOV polymerase RNA synthesis initiation and elongation. The structures demonstrate that THOV RNA transcription and replication are able to start with short dinucleotide primers and that the polymerase cap-snatching machinery is likely non-functional. Triggered by RNA synthesis, asymmetric THOV polymerase dimers can form without the involvement of host factors. We confirm that, distinctive from influenza viruses, THOV-polymerase RNA synthesis is weakly dependent of the host factors ANP32A/B/E in human cells. This study demonstrates varied mechanisms in RNA synthesis and host factor utilization among orthomyxoviruses, providing insights into the mechanisms behind thogotoviruses' broad-infectivity range. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8z8n.cif.gz | 314.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8z8n.ent.gz | 239.8 KB | Display | PDB format |
PDBx/mmJSON format | 8z8n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z8/8z8n ftp://data.pdbj.org/pub/pdb/validation_reports/z8/8z8n | HTTPS FTP |
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-Related structure data
Related structure data | 39849MC 8z85C 8z8jC 8z8xC 8z90C 8z97C 8z98C 8z9hC 8z9qC 8z9rC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 71623.445 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thogoto virus (isolate SiAr 126) / Gene: Segment 3 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P27194 |
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#2: Protein | Mass: 81432.664 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thogoto virus (isolate SiAr 126) / Gene: Segment 2 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: O41353, RNA-directed RNA polymerase |
#3: Protein | Mass: 94418.578 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thogoto virus (isolate SiAr 126) / Gene: Segment 1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9YNA4 |
#4: RNA chain | Mass: 5843.580 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Thogoto virus (isolate SiAr 126) |
#5: RNA chain | Mass: 5335.125 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Thogoto virus (isolate SiAr 126) |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Cryo-EM structure of Thogoto virus polymerase in transcription pre-initiation conformation 3 Type: COMPLEX / Entity ID: all / Source: MULTIPLE SOURCES |
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Source (natural) | Organism: Thogoto virus (isolate SiAr 126) |
Source (recombinant) | Organism: Spodoptera frugiperda (fall armyworm) |
Buffer solution | pH: 8 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: TFS KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2400 nm / Nominal defocus min: 600 nm |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: TFS FALCON 4i (4k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
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3D reconstruction | Resolution: 2.79 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 194071 / Symmetry type: POINT | ||||||||||||||||||||||||
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