+Open data
-Basic information
Entry | Database: PDB / ID: 9cpo | ||||||
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Title | Infectious bronchitis virus core polymerase complex | ||||||
Components |
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Keywords | VIRAL PROTEIN / IBV / Coronavirus / nsp12 / RdRp / RTC | ||||||
Function / homology | Function and homology information Transferases; Transferring one-carbon groups; Methyltransferases / Lyases; Phosphorus-oxygen lyases / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / 5'-3' DNA helicase activity / 3'-5'-RNA exonuclease activity / host cell endoplasmic reticulum-Golgi intermediate compartment / mRNA guanylyltransferase / omega peptidase activity / methyltransferase cap1 / DNA helicase ...Transferases; Transferring one-carbon groups; Methyltransferases / Lyases; Phosphorus-oxygen lyases / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / 5'-3' DNA helicase activity / 3'-5'-RNA exonuclease activity / host cell endoplasmic reticulum-Golgi intermediate compartment / mRNA guanylyltransferase / omega peptidase activity / methyltransferase cap1 / DNA helicase / endonuclease activity / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / ubiquitinyl hydrolase 1 / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / RNA helicase activity / host cell perinuclear region of cytoplasm / host cell endoplasmic reticulum membrane / viral protein processing / lyase activity / RNA helicase / induction by virus of host autophagy / cysteine-type endopeptidase activity / RNA-directed RNA polymerase / viral RNA genome replication / RNA-dependent RNA polymerase activity / DNA-templated transcription / ATP hydrolysis activity / proteolysis / RNA binding / zinc ion binding / ATP binding / membrane Similarity search - Function | ||||||
Biological species | Infectious bronchitis virus Severe acute respiratory syndrome coronavirus 2 | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å | ||||||
Authors | Hoferle, P.J. / Anderson, T.K. / Kirchdoerfer, R.N. | ||||||
Funding support | United States, 1items
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Citation | Journal: bioRxiv / Year: 2024 Title: A genus-specific nsp12 region impacts polymerase assembly in Alpha- and Gammacoronaviruses. Authors: Peter J Hoferle / Thomas K Anderson / Robert N Kirchdoerfer Abstract: Coronavirus relevancy for human health has surged over the past 20 years as they have a propensity for spillover into humans from animal reservoirs resulting in pandemics such as COVID-19. The ...Coronavirus relevancy for human health has surged over the past 20 years as they have a propensity for spillover into humans from animal reservoirs resulting in pandemics such as COVID-19. The diversity within the subfamily and high infection frequency in animal species worldwide creates a looming threat that calls for research across all genera within the subfamily. We sought to contribute to the limited structural knowledge within the genera and determined the structure of the viral core replication-transcription complex (RTC) from Infectious Bronchitis Virus (IBV) using single-particle cryo-EM. Comparison between our IBV structure with published RTC structures from other genera reveals structural differences across genera. Using biochemical assays, we characterized these differences and revealed their differing involvement in core RTC formation across different genera. Our findings highlight the value of cross-genera studies, as they show genera specific features in coronavirus genome replication. A broader knowledge of coronavirus replication will better prepare us for future coronavirus spillovers. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 9cpo.cif.gz | 511 KB | Display | PDBx/mmCIF format |
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PDB format | pdb9cpo.ent.gz | 414.8 KB | Display | PDB format |
PDBx/mmJSON format | 9cpo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cp/9cpo ftp://data.pdbj.org/pub/pdb/validation_reports/cp/9cpo | HTTPS FTP |
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-Related structure data
Related structure data | 45805MC 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
-Non-structural protein ... , 2 types, 3 molecules BDC
#2: Protein | Mass: 21567.691 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Infectious bronchitis virus / Gene: rep, 1a-1b / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P0C6Y3 #3: Protein | | Mass: 8014.378 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Infectious bronchitis virus / Gene: rep, 1a-1b / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P0C6Y3 |
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-RNA chain , 2 types, 2 molecules PT
#4: RNA chain | Mass: 9527.713 Da / Num. of mol.: 1 / Source method: obtained synthetically Source: (synth.) Severe acute respiratory syndrome coronavirus 2 |
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#5: RNA chain | Mass: 10566.281 Da / Num. of mol.: 1 / Source method: obtained synthetically Source: (synth.) Severe acute respiratory syndrome coronavirus 2 |
-Protein / Non-polymers , 2 types, 3 molecules A
#1: Protein | Mass: 107473.109 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Infectious bronchitis virus / Gene: rep, 1a-1b / Production host: Escherichia coli BL21 (bacteria) References: UniProt: P0C6Y3, RNA-directed RNA polymerase, mRNA guanylyltransferase |
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#6: Chemical |
-Details
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: Core polymerase complex of the infectious bronchitis virus composed of nsp12, nsp8, nsp7, and an dsRNA substrate Type: COMPLEX / Entity ID: #1-#5 / Source: RECOMBINANT |
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Molecular weight | Value: 0.194379 MDa / Experimental value: NO |
Source (natural) | Organism: Infectious bronchitis virus |
Source (recombinant) | Organism: Escherichia coli BL21 (bacteria) |
Buffer solution | pH: 8 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid type: EMS Lacey Carbon |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K |
-Electron microscopy imaging
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |
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Microscopy | Model: FEI TALOS ARCTICA |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 79000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm |
Image recording | Electron dose: 60 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
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3D reconstruction | Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 179183 / Symmetry type: POINT | ||||||||||||||||||||||||
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