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Yorodumi- PDB-7yed: In situ structure of polymerase complex of mammalian reovirus in ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7yed | |||||||||
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Title | In situ structure of polymerase complex of mammalian reovirus in the elongation state | |||||||||
Components |
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Keywords | VIRAL PROTEIN/RNA / mammalian reovirus / cryo-em / RNA dependent RNA polymerase / transcription / VIRAL PROTEIN / VIRAL PROTEIN-RNA complex | |||||||||
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 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 | 7yed.cif.gz | 3.4 MB | Display | PDBx/mmCIF format |
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PDB format | pdb7yed.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7yed.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7yed_validation.pdf.gz | 2.5 MB | Display | wwPDB validaton report |
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Full document | 7yed_full_validation.pdf.gz | 2.5 MB | Display | |
Data in XML | 7yed_validation.xml.gz | 431.5 KB | Display | |
Data in CIF | 7yed_validation.cif.gz | 701.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ye/7yed ftp://data.pdbj.org/pub/pdb/validation_reports/ye/7yed | HTTPS FTP |
-Related structure data
Related structure data | 33770MC 7yevC 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 #5: Protein | | Mass: 142472.953 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mammalian orthoreovirus 3 / References: UniProt: C9E870 #7: 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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-RNA chain , 3 types, 3 molecules MNT
#3: RNA chain | Mass: 6637.965 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Transcript RNA / Source: (synth.) Mammalian orthoreovirus 3 |
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#4: RNA chain | Mass: 11391.729 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Encoding RNA / Source: (synth.) Mammalian orthoreovirus 3 |
#6: RNA chain | Mass: 11391.729 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Template RNA / Source: (synth.) Mammalian orthoreovirus 3 |
-Non-polymers , 5 types, 26 molecules
#8: Chemical | ChemComp-ZN / #9: Chemical | ChemComp-SAM / #10: Chemical | ChemComp-GTP / #11: Chemical | ChemComp-UTP / | #12: Chemical | |
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-Details
Has ligand of interest | Y |
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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 |
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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
Software | Name: PHENIX / Version: (1.13_2998:phenix.real_space_refine) / Classification: refinement |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
3D reconstruction | Resolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 100968 / Symmetry type: POINT |
Refinement | Cross valid method: THROUGHOUT |
Displacement parameters | Biso max: 316.85 Å2 / Biso mean: 85.9855 Å2 / Biso min: 49.29 Å2 |