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Yorodumi- PDB-6v86: Parainfluenza virus 5 L-P complex with an alternate conformation ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6v86 | ||||||||||||||||||
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Title | Parainfluenza virus 5 L-P complex with an alternate conformation of the CD-MTase-CTD module | ||||||||||||||||||
Components |
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Keywords | VIRAL PROTEIN / POLYMERASE / METHYLTRANSFERASE / POLY-RIBONUCLEOTIDYLTRANSFERASE | ||||||||||||||||||
Function / homology | Function and homology information NNS virus cap methyltransferase / GDP polyribonucleotidyltransferase / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / virion component / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / host cell cytoplasm / RNA-directed RNA polymerase / RNA-dependent RNA polymerase activity / GTPase activity / ATP binding Similarity search - Function | ||||||||||||||||||
Biological species | Simian virus 5 | ||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.63 Å | ||||||||||||||||||
Authors | Abdella, R. / He, Y. | ||||||||||||||||||
Funding support | United States, 5items
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Citation | Journal: Proc Natl Acad Sci U S A / Year: 2020 Title: Structure of a paramyxovirus polymerase complex reveals a unique methyltransferase-CTD conformation. Authors: Ryan Abdella / Megha Aggarwal / Takashi Okura / Robert A Lamb / Yuan He / Abstract: Paramyxoviruses are enveloped, nonsegmented, negative-strand RNA viruses that cause a wide spectrum of human and animal diseases. The viral genome, packaged by the nucleoprotein (N), serves as a ...Paramyxoviruses are enveloped, nonsegmented, negative-strand RNA viruses that cause a wide spectrum of human and animal diseases. The viral genome, packaged by the nucleoprotein (N), serves as a template for the polymerase complex, composed of the large protein (L) and the homo-tetrameric phosphoprotein (P). The ∼250-kDa L possesses all enzymatic activities necessary for its function but requires P in vivo. Structural information is available for individual P domains from different paramyxoviruses, but how P interacts with L and how that affects the activity of L is largely unknown due to the lack of high-resolution structures of this complex in this viral family. In this study we determined the structure of the L-P complex from parainfluenza virus 5 (PIV5) at 4.3-Å resolution using cryoelectron microscopy, as well as the oligomerization domain (OD) of P at 1.4-Å resolution using X-ray crystallography. P-OD associates with the RNA-dependent RNA polymerase domain of L and protrudes away from it, while the X domain of one chain of P is bound near the L nucleotide entry site. The methyltransferase (MTase) domain and the C-terminal domain (CTD) of L adopt a unique conformation, positioning the MTase active site immediately above the poly-ribonucleotidyltransferase domain and near the likely exit site for the product RNA 5' end. Our study reveals a potential mechanism that mononegavirus polymerases may employ to switch between transcription and genome replication. This knowledge will assist in the design and development of antivirals against paramyxoviruses. | ||||||||||||||||||
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 | 6v86.cif.gz | 428.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6v86.ent.gz | 330.6 KB | Display | PDB format |
PDBx/mmJSON format | 6v86.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6v86_validation.pdf.gz | 789.8 KB | Display | wwPDB validaton report |
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Full document | 6v86_full_validation.pdf.gz | 855.6 KB | Display | |
Data in XML | 6v86_validation.xml.gz | 75.6 KB | Display | |
Data in CIF | 6v86_validation.cif.gz | 111.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v8/6v86 ftp://data.pdbj.org/pub/pdb/validation_reports/v8/6v86 | HTTPS FTP |
-Related structure data
Related structure data | 21096MC 6v85C 6vagC 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: 256195.672 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Simian virus 5 (strain W3) / Strain: W3 / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: Q88434, RNA-directed RNA polymerase, mRNA (guanine-N7)-methyltransferase, GDP polyribonucleotidyltransferase, EC: 2.1.1.296 | ||||
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#2: Protein | Mass: 42155.152 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Details: Chain F belongs to the same peptide as one of B, C, D or E, but the density is not well resolved enough to determine which chain it should associate with. Source: (gene. exp.) Simian virus 5 (strain W3) / Strain: W3 / Gene: P/V / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P11208 #3: Chemical | 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
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Molecular weight |
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Source (natural) |
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Source (recombinant) |
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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
Microscopy | Model: JEOL 3200FS |
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Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 80.8 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 717008 | ||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||
3D reconstruction | Resolution: 4.63 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 78547 / Symmetry type: POINT |