National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)
AI011219
United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)
AI104317
United States
Citation
Journal: Proc Natl Acad Sci U S A / Year: 2016 Title: Atomic structure of a rhinovirus C, a virus species linked to severe childhood asthma. Authors: Yue Liu / Marchel G Hill / Thomas Klose / Zhenguo Chen / Kelly Watters / Yury A Bochkov / Wen Jiang / Ann C Palmenberg / Michael G Rossmann / Abstract: Isolates of rhinovirus C (RV-C), a recently identified Enterovirus (EV) species, are the causative agents of severe respiratory infections among children and are linked to childhood asthma ...Isolates of rhinovirus C (RV-C), a recently identified Enterovirus (EV) species, are the causative agents of severe respiratory infections among children and are linked to childhood asthma exacerbations. The RV-C have been refractory to structure determination because they are difficult to propagate in vitro. Here, we report the cryo-EM atomic structures of the full virion and native empty particle (NEP) of RV-C15a. The virus has 60 "fingers" on the virus outer surface that probably function as dominant immunogens. Because the NEPs also display these fingers, they may have utility as vaccine candidates. A sequence-conserved surface depression adjacent to each finger forms a likely binding site for the sialic acid on its receptor. The RV-C, unlike other EVs, are resistant to capsid-binding antiviral compounds because the hydrophobic pocket in VP1 is filled with multiple bulky residues. These results define potential molecular determinants for designing antiviral therapeutics and vaccines.
Name: Rhinovirus C15a Details: The cDNA of RV-C15 isolate was used to produce RNA transcripts in vitro, which were then used for transfection in HeLa WisL cells. The resultant recombinant RV-C15 virus was adapted in HeLa ...Details: The cDNA of RV-C15 isolate was used to produce RNA transcripts in vitro, which were then used for transfection in HeLa WisL cells. The resultant recombinant RV-C15 virus was adapted in HeLa cells expressing the RV-C receptor CDHR3 via multiple passage. The derivative was the RV-C15a virus. Number of components: 4
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Component #1: virus, Rhinovirus C15a
Virus
Name: Rhinovirus C15a / Class: VIRUS-LIKE PARTICLE Details: The cDNA of RV-C15 isolate was used to produce RNA transcripts in vitro, which were then used for transfection in HeLa WisL cells. The resultant recombinant RV-C15 virus was adapted in HeLa ...Details: The cDNA of RV-C15 isolate was used to produce RNA transcripts in vitro, which were then used for transfection in HeLa WisL cells. The resultant recombinant RV-C15 virus was adapted in HeLa cells expressing the RV-C receptor CDHR3 via multiple passage. The derivative was the RV-C15a virus. Empty: Yes / Enveloped: No / Isolate: STRAIN
Mass
Theoretical: 5.8 MDa
Species
Species: Rhinovirus C15a
Source (engineered)
Expression System: Homo sapiens (human) / Vector: pC15 / Cell of expression system: HeLa
Source (natural)
Host Species: Homo sapiens (human)
Shell #1
Name of element: Capsid (p3) / Diameter: 300.0 Å / T number (triangulation number): 3
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Component #2: protein, Capsid protein VP1
Protein
Name: Capsid protein VP1 / Number of Copies: 1 / Recombinant expression: No
Mass
Theoretical: 31.802623 kDa
Source
Species: Rhinovirus C
Source (engineered)
Expression System: Homo sapiens (human)
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Component #3: protein, Capsid protein VP3
Protein
Name: Capsid protein VP3 / Number of Copies: 1 / Recombinant expression: No
Mass
Theoretical: 25.965037 kDa
Source
Species: Rhinovirus C
Source (engineered)
Expression System: Homo sapiens (human)
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Component #4: protein, Capsid protein VP0
Protein
Name: Capsid protein VP0 / Number of Copies: 1 / Recombinant expression: No
Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 25.7 e/Å2 / Illumination mode: FLOOD BEAM
Lens
Magnification: 14000.0 X (nominal) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD
Specimen Holder
Model: FEI TITAN KRIOS AUTOGRID HOLDER
Camera
Detector: GATAN K2 SUMMIT (4k x 4k)
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Image acquisition
Image acquisition
Number of digital images: 3614
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Image processing
Processing
Method: single particle reconstruction / Applied symmetry: I (icosahedral) / Number of projections: 3614
3D reconstruction
Software: jspr CTF correction: CTF correction was performed on the fly during 2D alignment and 3D reconstruction. Resolution: 3.16 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution estimation)
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Atomic model buiding
Modeling #1
Refinement protocol: rigid body / Target criteria: Correlation coefficient / Refinement space: REAL
In the structure databanks used in Yorodumi, some data are registered as the other names, "COVID-19 virus" and "2019-nCoV". Here are the details of the virus and the list of structure data.
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