+Open data
-Basic information
Entry | Database: PDB / ID: 6z0u | ||||||
---|---|---|---|---|---|---|---|
Title | CryoEM structure of the Chikungunya virus nsP1 complex | ||||||
Components | Polyprotein P1234 | ||||||
Keywords | VIRAL PROTEIN / Capping enzyme / monotopic membrane complex / membrane bending / membrane pore / replication complex / scaffold / Spherule formation / viral factory. | ||||||
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: 2.9 Å | ||||||
Authors | Reguera, J. / Jones, R. / Arranz-Avila, R. | ||||||
Funding support | France, 1items
| ||||||
Citation | Journal: Nature / Year: 2021 Title: Capping pores of alphavirus nsP1 gate membranous viral replication factories. Authors: Rhian Jones / Gabriel Bragagnolo / Rocío Arranz / Juan Reguera / Abstract: Positive-sense single-stranded RNA viruses, such as coronaviruses, flaviviruses and alphaviruses, carry out transcription and replication inside virus-induced membranous organelles within host cells. ...Positive-sense single-stranded RNA viruses, such as coronaviruses, flaviviruses and alphaviruses, carry out transcription and replication inside virus-induced membranous organelles within host cells. The remodelling of the host-cell membranes for the formation of these organelles is coupled to the membrane association of viral replication complexes and to RNA synthesis. These viral niches allow for the concentration of metabolites and proteins for the synthesis of viral RNA, and prevent the detection of this RNA by the cellular innate immune system. Here we present the cryo-electron microscopy structure of non-structural protein 1 (nsP1) of the alphavirus chikungunya virus, which is responsible for RNA capping and membrane binding of the viral replication machinery. The structure shows the enzyme in its active form, assembled in a monotopic membrane-associated dodecameric ring. The structure reveals the structural basis of the coupling between membrane binding, oligomerization and allosteric activation of the capping enzyme. The stoichiometry-with 12 active sites in a single complex-redefines viral replication complexes as RNA synthesis reactors. The ring shape of the complex implies it has a role in controlling access to the viral organelle and ensuring the exit of properly capped viral RNA. Our results provide high-resolution information about the membrane association of the replication machinery of positive-sense single-stranded RNA viruses, and open up avenues for the further characterization of viral replication on cell membranes and the generation of antiviral agents. | ||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6z0u.cif.gz | 1.8 MB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6z0u.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 6z0u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6z0u_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6z0u_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 6z0u_validation.xml.gz | 266 KB | Display | |
Data in CIF | 6z0u_validation.cif.gz | 412.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z0/6z0u ftp://data.pdbj.org/pub/pdb/validation_reports/z0/6z0u | HTTPS FTP |
-Related structure data
Related structure data | 11023MC 6z0vC M: map data used to model this data C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
|
---|---|
1 |
|
-Components
#1: Protein | Mass: 53064.031 Da / Num. of mol.: 24 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chikungunya virus strain S27-African prototype Production host: Baculovirus expression vector pFastBac1-HM References: UniProt: Q8JUX6, Transferases; Transferring one-carbon groups; Methyltransferases, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases, polynucleotide 5'- ...References: UniProt: Q8JUX6, Transferases; Transferring one-carbon groups; Methyltransferases, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases, polynucleotide 5'-phosphatase, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases, nucleoside-triphosphate phosphatase, RNA helicase, ADP-ribose 1''-phosphate phosphatase, polynucleotide adenylyltransferase, RNA-directed RNA polymerase #2: Chemical | ChemComp-ZN / #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Chikungunya NsP1 capping pore complex / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT | |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Molecular weight | Value: 1.4 MDa / Experimental value: NO | |||||||||||||||||||||||||
Source (natural) | Organism: Chikungunya virus strain S27-African prototype | |||||||||||||||||||||||||
Source (recombinant) | Organism: Baculovirus expression vector pFastBac1-HM | |||||||||||||||||||||||||
Buffer solution | pH: 7.6 | |||||||||||||||||||||||||
Buffer component |
| |||||||||||||||||||||||||
Specimen | Conc.: 0.25 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | |||||||||||||||||||||||||
Specimen support | Grid type: Quantifoil R2/2 | |||||||||||||||||||||||||
Vitrification | Instrument: LEICA EM CPC / Cryogen name: ETHANE-PROPANE Details: 3ul of sample was spotted onto the grid and hand blotted prior to plunge freezing. |
-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 magnification: 165000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 5 sec. / Electron dose: 38.5 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 5148 |
EM imaging optics | Energyfilter name: GIF Quantum LS / Energyfilter slit width: 20 eV |
Image scans | Width: 3838 / Height: 3710 / Movie frames/image: 40 / Used frames/image: 1-40 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
EM software |
| ||||||||||||||||||||||||||||||||||||
CTF correction | Details: CTF was estimated from movie frames aligned without dose-weighting. Per particle CTF correction was also performed with polished particles. Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 263415 Details: Autopicking following generation of templates from 2D class averages | ||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: D12 (2x12 fold dihedral) | ||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 47338 / Num. of class averages: 1 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: AB INITIO MODEL / Space: REAL / Target criteria: CC | ||||||||||||||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 50.6 Å2 | ||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|