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Yorodumi- PDB-6l42: Structure of severe fever with thrombocytopenia syndrome virus L ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6l42 | |||||||||
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Title | Structure of severe fever with thrombocytopenia syndrome virus L protein | |||||||||
Components | RNA polymerase | |||||||||
Keywords | VIRAL PROTEIN / polymease / VIRUS | |||||||||
Function / homology | Function and homology information host cell endoplasmic reticulum / virion component / host cell endoplasmic reticulum-Golgi intermediate compartment / host cell Golgi apparatus / Hydrolases; Acting on ester bonds / hydrolase activity / RNA-directed RNA polymerase / viral RNA genome replication / RNA-dependent RNA polymerase activity / DNA-templated transcription / metal ion binding Similarity search - Function | |||||||||
Biological species | Phlebovirus WCH/97/HN/China/2011 | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å | |||||||||
Authors | Wang, P. / Lou, Z. | |||||||||
Funding support | China, 1items
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Citation | Journal: Nat Microbiol / Year: 2020 Title: Structure of severe fever with thrombocytopenia syndrome virus L protein elucidates the mechanisms of viral transcription initiation. Authors: Panpan Wang / Lu Liu / Aijun Liu / Liming Yan / Yong He / Shu Shen / Mingxu Hu / Yu Guo / Haiguang Liu / Chuang Liu / Yinying Lu / Peiyi Wang / Fei Deng / Zihe Rao / Zhiyong Lou / Abstract: Segmented negative-sense RNA viruses (sNSRVs) encode a single-polypeptide polymerase (L protein) or a heterotrimeric polymerase complex to cannibalize host messenger RNA cap structures serving as ...Segmented negative-sense RNA viruses (sNSRVs) encode a single-polypeptide polymerase (L protein) or a heterotrimeric polymerase complex to cannibalize host messenger RNA cap structures serving as primers of transcription, and catalyse RNA synthesis. Here, we report the full-length structure of the severe fever with thrombocytopaenia syndrome virus (SFTSV) L protein, as determined by cryogenic electron microscopy at 3.4 Å, leading to an atomic model harbouring three functional parts (an endonuclease, an RNA-dependent RNA polymerase and a cap-binding domain) and two structural domains (an arm domain with a blocker motif and a carboxy-terminal lariat domain). The SFTSV L protein has a compact architecture in which its cap-binding pocket is surprisingly occupied by an Arg finger of the blocker motif, and the endonuclease active centre faces back towards the cap-binding pocket, suggesting that domain rearrangements are necessary to acquire the pre-initiation state of the active site. Our results provide insight into the complete architecture of sNSRV-encoded L protein and further the understanding of sNSRV transcription initiation. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6l42.cif.gz | 357.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6l42.ent.gz | 272.8 KB | Display | PDB format |
PDBx/mmJSON format | 6l42.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l4/6l42 ftp://data.pdbj.org/pub/pdb/validation_reports/l4/6l42 | HTTPS FTP |
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-Related structure data
Related structure data | 0828MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 238813.797 Da / Num. of mol.: 1 / Mutation: Q1314E Source method: isolated from a genetically manipulated source Source: (gene. exp.) Phlebovirus WCH/97/HN/China/2011 Production host: Insect expression vector pBlueBacmsGCB1His (others) References: UniProt: I0DF35 |
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#2: Chemical | ChemComp-MG / |
Has ligand of interest | N |
-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: Virus polymerase / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT |
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Source (natural) | Organism: Phlebovirus WCH/97/HN/China/2011 |
Source (recombinant) | Organism: Insect expression vector pBlueBacmsGCB1His (others) |
Buffer solution | pH: 7.5 |
Specimen | Conc.: 0.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE / Humidity: 100 % |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company | |||||||||||||||
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Microscopy | Model: FEI TITAN KRIOS | |||||||||||||||
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER | |||||||||||||||
Electron lens | Mode: BRIGHT FIELD | |||||||||||||||
Image recording |
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-Processing
Software | Name: PHENIX / Version: 1.16_3549: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 147344 / Symmetry type: POINT | ||||||||||||||||||||||||
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