[English] 日本語
Yorodumi- PDB-7yg7: Structure of the Spring Viraemia of Carp Virus ribonucleoprotein ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7yg7 | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Structure of the Spring Viraemia of Carp Virus ribonucleoprotein Complex | ||||||||||||
Components |
| ||||||||||||
Keywords | VIRUS LIKE PARTICLE/RNA / Ribonucleoprotein / Complex / VIRUS / VIRUS LIKE PARTICLE-RNA complex | ||||||||||||
Function / homology | RNA / RNA (> 10) Function and homology information | ||||||||||||
Biological species | Sprivivirus cyprinus Trichoplusia ni (cabbage looper) | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å | ||||||||||||
Authors | Liu, B. / Wang, Z.X. / Yang, T. / Yu, D.Q. / Ouyang, Q. | ||||||||||||
Funding support | China, 3items
| ||||||||||||
Citation | Journal: J Virol / Year: 2023 Title: Structure of the Spring Viraemia of Carp Virus Ribonucleoprotein Complex Reveals Its Assembly Mechanism and Application in Antiviral Drug Screening. Authors: Zhao-Xi Wang / Bing Liu / Tian Yang / Daqi Yu / Chu Zhang / Liming Zheng / Jin Xie / Bin Liu / Mengxi Liu / Hailin Peng / Luhua Lai / Qi Ouyang / Songying Ouyang / Yong-An Zhang / Abstract: Spring viremia of carp virus (SVCV) is a highly pathogenic infecting the common carp, yet neither a vaccine nor effective therapies are available to treat spring viremia of carp (SVC). Like all ...Spring viremia of carp virus (SVCV) is a highly pathogenic infecting the common carp, yet neither a vaccine nor effective therapies are available to treat spring viremia of carp (SVC). Like all negative-sense viruses, SVCV contains an RNA genome that is encapsidated by the nucleoprotein (N) in the form of a ribonucleoprotein (RNP) complex, which serves as the template for viral replication and transcription. Here, the three-dimensional (3D) structure of SVCV RNP was resolved through cryo-electron microscopy (cryo-EM) at a resolution of 3.7 Å. RNP assembly was stabilized by N and C loops; RNA was wrapped in the groove between the N and C lobes with 9 nt nucleotide per protomer. Combined with mutational analysis, our results elucidated the mechanism of RNP formation. The RNA binding groove of SVCV N was used as a target for drug virtual screening, and it was found suramin had a good antiviral effect. This study provided insights into RNP assembly, and anti-SVCV drug screening was performed on the basis of this structure, providing a theoretical basis and efficient drug screening method for the prevention and treatment of SVC. Aquaculture accounts for about 70% of global aquatic products, and viral diseases severely harm the development of aquaculture industry. Spring viremia of carp virus (SVCV) is the pathogen causing highly contagious spring viremia of carp (SVC) disease in cyprinids, especially common carp (), yet neither a vaccine nor effective therapies are available to treat this disease. In this study, we have elucidated the mechanism of SVCV ribonucleoprotein complex (RNP) formation by resolving the 3D structure of SVCV RNP and screened antiviral drugs based on the structure. It is found that suramin could competitively bind to the RNA binding groove and has good antiviral effects both and . Our study provides a template for rational drug discovery efforts to treat and prevent SVCV infections. | ||||||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7yg7.cif.gz | 791.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7yg7.ent.gz | 669.8 KB | Display | PDB format |
PDBx/mmJSON format | 7yg7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7yg7_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 7yg7_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 7yg7_validation.xml.gz | 115.4 KB | Display | |
Data in CIF | 7yg7_validation.cif.gz | 178.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yg/7yg7 ftp://data.pdbj.org/pub/pdb/validation_reports/yg/7yg7 | HTTPS FTP |
-Related structure data
Related structure data | 33810MC 7xpnC M: map data used to model this data C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
|
---|---|
1 |
|
-Components
#1: Protein | Mass: 46621.160 Da / Num. of mol.: 11 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sprivivirus cyprinus / Cell line (production host): High Five / Production host: Trichoplusia ni (cabbage looper) #2: RNA chain | | Mass: 30265.480 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trichoplusia ni (cabbage looper) |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component |
| ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Molecular weight | Experimental value: NO | ||||||||||||||||||||||||
Source (natural) |
| ||||||||||||||||||||||||
Source (recombinant) | Organism: Trichoplusia ni (cabbage looper) / Cell: High Five | ||||||||||||||||||||||||
Buffer solution | pH: 7.5 | ||||||||||||||||||||||||
Specimen | Conc.: 0.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||
Specimen support | Grid material: GOLD / Grid mesh size: 400 divisions/in. / Grid type: C-flat-1.2/1.3 | ||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 300 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
---|---|
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: 3000 nm / Nominal defocus min: 700 nm |
Image recording | Electron dose: 45 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.20.1_4487: / Classification: refinement | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
CTF correction | Type: NONE | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 614458 / Symmetry type: POINT | ||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL | ||||||||||||||||||||||||
Refine LS restraints |
|