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Yorodumi- PDB-7fgi: Cryo-EM Structure of Chikungunya Virus Nonstructural Protein 1 wi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7fgi | |||||||||
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Title | Cryo-EM Structure of Chikungunya Virus Nonstructural Protein 1 with m7Gppp-AU | |||||||||
Components |
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Keywords | VIRAL PROTEIN/RNA / nonstructural protein / Chikungunya virus / RNA cap / replication / VIRAL PROTEIN / VIRAL PROTEIN-RNA complex | |||||||||
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 / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / cysteine-type peptidase activity / Transferases; Transferring one-carbon groups; Methyltransferases / host cell cytoplasmic vesicle membrane / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / nucleoside-triphosphate phosphatase / methylation / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / RNA helicase activity / RNA helicase / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / symbiont-mediated suppression of host innate immune response / RNA-directed RNA polymerase / viral RNA genome replication / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / DNA-templated transcription / GTP binding / host cell nucleus / 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 synthetic construct (others) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.51 Å | |||||||||
Authors | Zhang, K. / Law, M.C.Y. / Nguyen, T.M. / Tan, Y.B. / Wirawan, M. / Law, Y.S. / Luo, D.H. | |||||||||
Citation | Journal: Cell Rep / Year: 2022 Title: Molecular basis of specific viral RNA recognition and 5'-end capping by the Chikungunya virus nsP1. Authors: Kuo Zhang / Michelle Cheok Yien Law / Trinh Mai Nguyen / Yaw Bia Tan / Melissa Wirawan / Yee-Song Law / Lak Shin Jeong / Dahai Luo / Abstract: Many viruses encode RNA-modifying enzymes to edit the 5' end of viral RNA to mimic the cellular mRNA for effective protein translation, genome replication, and evasion of the host defense mechanisms. ...Many viruses encode RNA-modifying enzymes to edit the 5' end of viral RNA to mimic the cellular mRNA for effective protein translation, genome replication, and evasion of the host defense mechanisms. Alphavirus nsP1 synthesizes the 5' end Cap-0 structure of viral RNAs. However, the molecular basis of the capping process remains unclear. We determine high-resolution cryoelectron microscopy (cryo-EM) structures of Chikungunya virus nsP1 in complex with m7GTP/SAH, covalently attached m7GMP, and Cap-0 viral RNA. These structures reveal details of viral-RNA-capping reactions and uncover a sequence-specific virus RNA-recognition pattern that, in turn, regulates viral-RNA-capping efficiency to ensure optimal genome replication and subgenomic RNA transcription. This sequence-specific enzyme-RNA pairing is conserved across all alphaviruses. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7fgi.cif.gz | 905.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7fgi.ent.gz | 725.3 KB | Display | PDB format |
PDBx/mmJSON format | 7fgi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7fgi_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 7fgi_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 7fgi_validation.xml.gz | 121 KB | Display | |
Data in CIF | 7fgi_validation.cif.gz | 185.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fg/7fgi ftp://data.pdbj.org/pub/pdb/validation_reports/fg/7fgi | HTTPS FTP |
-Related structure data
Related structure data | 31582MC 7fggC 7fghC 7x01C 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
#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 #2: RNA chain | Mass: 1375.840 Da / Num. of mol.: 12 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #3: Chemical | ChemComp-ZN / #4: Chemical | ChemComp-SAH / #5: Chemical | ChemComp-MG / 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: 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 |
Image recording | Electron dose: 70 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.18.2_3874: / Classification: refinement | ||||||||||||||||||||||||
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Image processing | Details: C12 | ||||||||||||||||||||||||
CTF correction | Type: NONE | ||||||||||||||||||||||||
3D reconstruction | Resolution: 2.51 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 61617 / Symmetry type: POINT | ||||||||||||||||||||||||
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