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Yorodumi- PDB-7ell: In situ structure of capping enzyme lambda2, penetration protein ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7ell | |||||||||||||||||||||||||||
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Title | In situ structure of capping enzyme lambda2, penetration protein mu1 of mammalian reovirus capsid asymmetric unit. | |||||||||||||||||||||||||||
Components |
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Keywords | VIRAL PROTEIN/TRANSFERASE / mammalian reovirus 3 / capping enzyme lambda2 / penetration protein mu1 / VIRUS / VIRAL PROTEIN-TRANSFERASE complex | |||||||||||||||||||||||||||
Function / homology | Function and homology information host cell surface binding / viral outer capsid / permeabilization of host organelle membrane involved in viral entry into host cell / symbiont entry into host cell via permeabilization of inner membrane / : / mRNA guanylyltransferase activity / mRNA guanylyltransferase / mRNA (guanine-N7)-methyltransferase / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / GTP binding / ATP binding Similarity search - Function | |||||||||||||||||||||||||||
Biological species | Mammalian orthoreovirus 3 | |||||||||||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 Å | |||||||||||||||||||||||||||
Authors | Zhou, Z.H. / Pan, M. | |||||||||||||||||||||||||||
Funding support | United States, 8items
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Citation | Journal: Nat Commun / Year: 2021 Title: Asymmetric reconstruction of mammalian reovirus reveals interactions among RNA, transcriptional factor µ2 and capsid proteins. Authors: Muchen Pan / Ana L Alvarez-Cabrera / Joon S Kang / Lihua Wang / Chunhai Fan / Z Hong Zhou / Abstract: Mammalian reovirus (MRV) is the prototypical member of genus Orthoreovirus of family Reoviridae. However, lacking high-resolution structures of its RNA polymerase cofactor μ2 and infectious ...Mammalian reovirus (MRV) is the prototypical member of genus Orthoreovirus of family Reoviridae. However, lacking high-resolution structures of its RNA polymerase cofactor μ2 and infectious particle, limits understanding of molecular interactions among proteins and RNA, and their contributions to virion assembly and RNA transcription. Here, we report the 3.3 Å-resolution asymmetric reconstruction of transcribing MRV and in situ atomic models of its capsid proteins, the asymmetrically attached RNA-dependent RNA polymerase (RdRp) λ3, and RdRp-bound nucleoside triphosphatase μ2 with a unique RNA-binding domain. We reveal molecular interactions among virion proteins and genomic and messenger RNA. Polymerase complexes in three Spinoreovirinae subfamily members are organized with different pseudo-D symmetries to engage their highly diversified genomes. The above interactions and those between symmetry-mismatched receptor-binding σ1 trimers and RNA-capping λ2 pentamers balance competing needs of capsid assembly, external protein removal, and allosteric triggering of endogenous RNA transcription, before, during and after infection, respectively. | |||||||||||||||||||||||||||
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 | 7ell.cif.gz | 1.3 MB | Display | PDBx/mmCIF format |
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PDB format | pdb7ell.ent.gz | 1.1 MB | Display | PDB format |
PDBx/mmJSON format | 7ell.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/el/7ell ftp://data.pdbj.org/pub/pdb/validation_reports/el/7ell | HTTPS FTP |
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-Related structure data
Related structure data | 31184MC 7elhC 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/peptide | Mass: 4050.441 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Source: (natural) Mammalian orthoreovirus 3 / References: UniProt: F1ARM5 #2: Protein | Mass: 72228.719 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Source: (natural) Mammalian orthoreovirus 3 / References: UniProt: F1ARM5 #3: Protein | | Mass: 143998.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mammalian orthoreovirus 3 References: UniProt: A0A0B5CUT9, mRNA (guanine-N7)-methyltransferase, mRNA guanylyltransferase #4: Chemical | ChemComp-MYR / 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 | Name: Mammalian orthoreovirus 3 Dearing / Type: VIRUS / Entity ID: #3 / Source: NATURAL |
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Source (natural) | Organism: Mammalian orthoreovirus 3 Dearing |
Details of virus | Empty: NO / Enveloped: NO / Isolate: SEROTYPE / Type: VIRION |
Buffer solution | pH: 7.4 |
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 FIELDBright-field microscopy |
Image recording | Electron dose: 56 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: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 61861 / Symmetry type: POINT |
Refinement | Highest resolution: 3.8 Å |