+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 / host cell endoplasmic reticulum-Golgi intermediate compartment / 3'-5'-RNA exonuclease activity / mRNA guanylyltransferase / omega peptidase activity / methyltransferase cap1 / endonuclease activity ...Transferases; Transferring one-carbon groups; Methyltransferases / Lyases; Phosphorus-oxygen lyases / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / 5'-3' DNA helicase activity / host cell endoplasmic reticulum-Golgi intermediate compartment / 3'-5'-RNA exonuclease activity / mRNA guanylyltransferase / omega peptidase activity / methyltransferase cap1 / endonuclease activity / DNA helicase / 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 / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / 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: Hoferle, P.J. / Anderson, T.K. / Kirchdoerfer, R.N. | ||||||
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 | 510.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb9cpo.ent.gz | 414.7 KB | Display | PDB format |
PDBx/mmJSON format | 9cpo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 9cpo_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 9cpo_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 9cpo_validation.xml.gz | 49.8 KB | Display | |
Data in CIF | 9cpo_validation.cif.gz | 76 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cp/9cpo ftp://data.pdbj.org/pub/pdb/validation_reports/cp/9cpo | HTTPS FTP |
-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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