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Yorodumi- PDB-8jce: Cryo-EM Structure of Chikungunya Virus Nonstructural Protein 1 wi... -
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-Basic information
Entry | Database: PDB / ID: 8jce | ||||||
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Title | Cryo-EM Structure of Chikungunya Virus Nonstructural Protein 1 with m7GpppAmU | ||||||
Components | mRNA-capping enzyme nsP1 | ||||||
Keywords | VIRAL PROTEIN / nonstructural protein / Chikungunya virus / RNA cap / replication | ||||||
Function / homology | Function and homology information host cell filopodium / ADP-ribose 1''-phosphate phosphatase / mRNA methyltransferase activity / mRNA 5'-triphosphate monophosphatase activity / mRNA 5'-phosphatase / polynucleotide 5'-phosphatase activity / polynucleotide adenylyltransferase / poly(A) RNA polymerase activity / regulation of cytoskeleton organization / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity ...host cell filopodium / ADP-ribose 1''-phosphate phosphatase / mRNA methyltransferase activity / mRNA 5'-triphosphate monophosphatase activity / mRNA 5'-phosphatase / polynucleotide 5'-phosphatase activity / polynucleotide adenylyltransferase / poly(A) RNA polymerase activity / regulation of cytoskeleton organization / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / 7-methylguanosine mRNA capping / cysteine-type peptidase activity / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / Transferases; Transferring one-carbon groups; Methyltransferases / host cell cytoplasmic vesicle membrane / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / nucleoside-triphosphate phosphatase / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / RNA helicase activity / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / RNA helicase / RNA-directed RNA polymerase / viral RNA genome replication / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / DNA-templated transcription / host cell nucleus / GTP binding / host cell plasma membrane / ATP hydrolysis activity / proteolysis / RNA binding / ATP binding / membrane / metal ion binding Similarity search - Function | ||||||
Biological species | Chikungunya virus strain S27-African prototype | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.41 Å | ||||||
Authors | Zhang, K. / Law, M.C.Y. / Nguyen, T.M. / Tan, Y.B. / Wirawan, M. / Law, Y.S. / Luo, D.H. | ||||||
Funding support | 1items
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Citation | Journal: J Biol Chem / Year: 2023 Title: Chikungunya virus nonstructural protein 1 is a versatile RNA capping and decapping enzyme. Authors: Michelle Cheok Yien Law / Kuo Zhang / Yaw Bia Tan / Trinh Mai Nguyen / Dahai Luo / Abstract: Chikungunya virus (CHIKV) nonstructural protein 1 (nsP1) contains both the N7-guanine methyltransferase and guanylyltransferase activities and catalyzes the 5' end cap formation of viral RNAs. To ...Chikungunya virus (CHIKV) nonstructural protein 1 (nsP1) contains both the N7-guanine methyltransferase and guanylyltransferase activities and catalyzes the 5' end cap formation of viral RNAs. To further understand its catalytic activity and role in virus-host interaction, we demonstrate that purified recombinant CHIKV nsP1 can reverse the guanylyl transfer reaction and remove the mGMP from a variety of capped RNA substrates including host mRNAs. We then provide the structural basis of this function with a high-resolution cryo-EM structure of nsP1 in complex with the unconventional cap-1 substrate RNA mGpppAU. We show that the 5'ppRNA species generated by decapping can trigger retinoic acid-inducible gene I-mediated interferon response. We further demonstrate that the decapping activity is conserved among the alphaviral nsP1s. To our knowledge, this is a new mechanism through which alphaviruses activate the antiviral immune response. This decapping activity could promote cellular mRNA degradation and facilitate viral gene expression, which is functionally analogous to the cap-snatching mechanism by influenza virus. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8jce.cif.gz | 961.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8jce.ent.gz | 805 KB | Display | PDB format |
PDBx/mmJSON format | 8jce.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8jce_validation.pdf.gz | 3 MB | Display | wwPDB validaton report |
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Full document | 8jce_full_validation.pdf.gz | 3 MB | Display | |
Data in XML | 8jce_validation.xml.gz | 145.8 KB | Display | |
Data in CIF | 8jce_validation.cif.gz | 213.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jc/8jce ftp://data.pdbj.org/pub/pdb/validation_reports/jc/8jce | HTTPS FTP |
-Related structure data
Related structure data | 36159MC 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 , 1 types, 12 molecules ABCDEFGHIJKL
#1: Protein | Mass: 61989.477 Da / Num. of mol.: 12 / Mutation: H37A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chikungunya virus strain S27-African prototype Production host: Homo sapiens (human) References: UniProt: Q8JUX6, Transferases; Transferring one-carbon groups; Methyltransferases, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases |
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-Non-polymers , 5 types, 636 molecules
#2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-SAH / #4: Chemical | ChemComp-YG4 / [( #5: Chemical | ChemComp-MG / #6: Water | ChemComp-HOH / | |
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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 | Name: Nonstructural Protein 1 / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT |
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Source (natural) | Organism: Chikungunya virus strain S27-African prototype |
Source (recombinant) | Organism: Homo sapiens (human) |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K |
-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: 3500 nm / Nominal defocus min: 600 nm |
Image recording | Electron dose: 70 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
CTF correction | Type: NONE | ||||||||||||||||||||||||
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3D reconstruction | Resolution: 2.41 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 70128 / Symmetry type: POINT | ||||||||||||||||||||||||
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