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Yorodumi- PDB-7yev: In situ structure of polymerase complex of mammalian reovirus in ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7yev | |||||||||
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Title | In situ structure of polymerase complex of mammalian reovirus in the pre-elongation state | |||||||||
Components |
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Keywords | VIRAL PROTEIN / mammalian reovirus / cryo-em / RNA dependent RNA polymerase / transcription | |||||||||
Function / homology | Function and homology information viral inner capsid / host cytoskeleton / viral outer capsid / 7-methylguanosine mRNA capping / viral genome replication / viral capsid / mRNA guanylyltransferase activity / viral nucleocapsid / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / host cell cytoplasm ...viral inner capsid / host cytoskeleton / viral outer capsid / 7-methylguanosine mRNA capping / viral genome replication / viral capsid / mRNA guanylyltransferase activity / viral nucleocapsid / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / host cell cytoplasm / RNA helicase activity / hydrolase activity / RNA-directed RNA polymerase / RNA-dependent RNA polymerase activity / GTP binding / structural molecule activity / RNA binding / ATP binding Similarity search - Function | |||||||||
Biological species | Mammalian orthoreovirus 3 | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å | |||||||||
Authors | Bao, K.Y. / Zhang, X.L. / Li, D.Y. / Zhu, P. | |||||||||
Funding support | China, 2items
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Citation | Journal: Proc Natl Acad Sci U S A / Year: 2022 Title: In situ structures of polymerase complex of mammalian reovirus illuminate RdRp activation and transcription regulation. Authors: Keyan Bao / Xueli Zhang / Dongyu Li / Wei Sun / Zhenzhao Sun / Jingfei Wang / Ping Zhu / Abstract: Mammalian reovirus (reovirus) is a multilayered, turreted member of characterized by transcription of dsRNA genome within the innermost capsid shell. Here, we present high-resolution in situ ...Mammalian reovirus (reovirus) is a multilayered, turreted member of characterized by transcription of dsRNA genome within the innermost capsid shell. Here, we present high-resolution in situ structures of reovirus transcriptase complex in an intact double-layered virion, and in the uncoated single-layered core particles in the unloaded, reloaded, pre-elongation, and elongation states, respectively, obtained by cryo-electron microscopy and sub-particle reconstructions. At the template entry of RNA-dependent RNA polymerase (RdRp), the RNA-loading region gets flexible after uncoating resulting in the unloading of terminal genomic RNA and inactivity of transcription. However, upon adding transcriptional substrates, the RNA-loading region is recovered leading the RNAs loaded again. The priming loop in RdRp was found to play a critical role in regulating transcription, which hinders the elongation of transcript in virion and triggers the rearrangement of RdRp C-terminal domain (CTD) during elongation, resulting in splitting of template-transcript hybrid and opening of transcript exit. With the integration of these structures, a transcriptional model of reovirus with five states is proposed. Our structures illuminate the RdRp activation and regulation of the multilayered turreted reovirus. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7yev.cif.gz | 3.2 MB | Display | PDBx/mmCIF format |
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PDB format | pdb7yev.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7yev.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7yev_validation.pdf.gz | 2 MB | Display | wwPDB validaton report |
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Full document | 7yev_full_validation.pdf.gz | 2 MB | Display | |
Data in XML | 7yev_validation.xml.gz | 406.6 KB | Display | |
Data in CIF | 7yev_validation.cif.gz | 645.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ye/7yev ftp://data.pdbj.org/pub/pdb/validation_reports/ye/7yev | HTTPS FTP |
-Related structure data
Related structure data | 33778MC 7yedC 7yezC 7yf0C 7yfeC 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
-Protein , 4 types, 22 molecules 12345ABCDEabcdeHIJKLRU
#1: Protein | Mass: 141801.297 Da / Num. of mol.: 15 / Source method: isolated from a natural source / Source: (natural) Mammalian orthoreovirus 3 / References: UniProt: C9E874, RNA helicase #2: Protein | Mass: 143963.438 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Mammalian orthoreovirus 3 / References: UniProt: C9E871 #3: Protein | | Mass: 142472.953 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mammalian orthoreovirus 3 / References: UniProt: C9E870, RNA-directed RNA polymerase #4: Protein | | Mass: 83434.266 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mammalian orthoreovirus 3 / References: UniProt: C9E872 |
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-Non-polymers , 2 types, 18 molecules
#5: Chemical | ChemComp-ZN / #6: Chemical | ChemComp-SAM / |
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-Details
Has ligand of interest | N |
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-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: Mammalian orthoreovirus 3 / Type: VIRUS / Entity ID: #4, #3, #1-#2 / Source: NATURAL |
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Source (natural) | Organism: Mammalian orthoreovirus 3 |
Details of virus | Empty: NO / Enveloped: NO / Isolate: STRAIN / Type: VIRION |
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: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 1800 nm / Nominal defocus min: 1500 nm |
Image recording | Electron dose: 30 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 45544 / Symmetry type: POINT |