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- PDB-5k0u: CryoEM structure of the full virion of a human rhinovirus C -

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Basic information

Entry
Database: PDB / ID: 5k0u
TitleCryoEM structure of the full virion of a human rhinovirus C
Components
  • Capsid protein VP1
  • Capsid protein VP2
  • Capsid protein VP3
  • Capsid protein VP4
KeywordsVIRUS / jelly roll
Function / homology
Function and homology information


symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / ribonucleoside triphosphate phosphatase activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / nucleoside-triphosphate phosphatase / channel activity ...symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / ribonucleoside triphosphate phosphatase activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / nucleoside-triphosphate phosphatase / channel activity / monoatomic ion transmembrane transport / DNA replication / RNA helicase activity / endocytosis involved in viral entry into host cell / symbiont-mediated activation of host autophagy / RNA-directed RNA polymerase / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / DNA-templated transcription / virion attachment to host cell / host cell nucleus / structural molecule activity / proteolysis / RNA binding / zinc ion binding / ATP binding / membrane
Similarity search - Function
Picornavirus coat protein VP4 superfamily / Jelly Rolls - #20 / Picornavirus coat protein / Poliovirus 3A protein-like / Poliovirus 3A protein like / Picornavirus 2B protein / Poliovirus core protein 3a, soluble domain / Picornavirus 2B protein / Peptidase C3, picornavirus core protein 2A / Picornavirus core protein 2A ...Picornavirus coat protein VP4 superfamily / Jelly Rolls - #20 / Picornavirus coat protein / Poliovirus 3A protein-like / Poliovirus 3A protein like / Picornavirus 2B protein / Poliovirus core protein 3a, soluble domain / Picornavirus 2B protein / Peptidase C3, picornavirus core protein 2A / Picornavirus core protein 2A / Picornavirus coat protein VP4 / Picornavirus coat protein (VP4) / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / Picornavirus capsid / picornavirus capsid protein / Helicase, superfamily 3, single-stranded RNA virus / Superfamily 3 helicase of positive ssRNA viruses domain profile. / Helicase, superfamily 3, single-stranded DNA/RNA virus / RNA helicase / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / RNA-directed RNA polymerase, C-terminal domain / Viral RNA-dependent RNA polymerase / Reverse transcriptase/Diguanylate cyclase domain / Jelly Rolls / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / Sandwich / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
Biological speciesRhinovirus C
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.79 Å
AuthorsLiu, Y. / Hill, M.G. / Klose, T. / Chen, Z. / Watters, K.E. / Jiang, W. / Palmenberg, A.C. / Rossmann, M.G.
Funding support United States, 2items
OrganizationGrant numberCountry
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
CitationJournal: 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.
History
DepositionMay 17, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 13, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 31, 2016Group: Database references
Revision 1.2Sep 13, 2017Group: Author supporting evidence / Data collection / Category: em_software / pdbx_audit_support
Item: _em_software.name / _pdbx_audit_support.funding_organization
Revision 1.3Jul 18, 2018Group: Data collection / Category: em_software / Item: _em_software.name
Revision 1.4Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type

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Structure visualization

Movie
  • Biological unit as complete icosahedral assembly
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  • Biological unit as icosahedral pentamer
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  • Biological unit as icosahedral 23 hexamer
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  • Deposited structure unit
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  • Simplified surface model + fitted atomic model
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Structure viewerMolecule:
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Assembly

Deposited unit
A: Capsid protein VP1
B: Capsid protein VP3
C: Capsid protein VP2
D: Capsid protein VP4


Theoretical massNumber of molelcules
Total (without water)94,0334
Polymers94,0334
Non-polymers00
Water1,08160
1
A: Capsid protein VP1
B: Capsid protein VP3
C: Capsid protein VP2
D: Capsid protein VP4
x 60


Theoretical massNumber of molelcules
Total (without water)5,641,985240
Polymers5,641,985240
Non-polymers00
Water4,324240
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
2


  • Idetical with deposited unit
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Capsid protein VP1
B: Capsid protein VP3
C: Capsid protein VP2
D: Capsid protein VP4
x 5


  • icosahedral pentamer
  • 470 kDa, 20 polymers
Theoretical massNumber of molelcules
Total (without water)470,16520
Polymers470,16520
Non-polymers00
Water36020
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: Capsid protein VP1
B: Capsid protein VP3
C: Capsid protein VP2
D: Capsid protein VP4
x 6


  • icosahedral 23 hexamer
  • 564 kDa, 24 polymers
Theoretical massNumber of molelcules
Total (without water)564,19824
Polymers564,19824
Non-polymers00
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
5


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))

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Components

#1: Protein Capsid protein VP1


Mass: 31802.623 Da / Num. of mol.: 1 / Fragment: UNP residues 568-846 / Mutation: T125K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhinovirus C / Cell line: transduced HeLa expressing CDHR3 / Cell line (production host): HeLa WisL / Production host: Homo sapiens (human) / References: UniProt: E5D8F2
#2: Protein Capsid protein VP3


Mass: 25965.037 Da / Num. of mol.: 1 / Fragment: UNP residues 333-567
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhinovirus C / Cell line: transduced HeLa expressing CDHR3 / Cell line (production host): HeLa WisL / Production host: Homo sapiens (human) / References: UniProt: E5D8F2
#3: Protein Capsid protein VP2


Mass: 29090.658 Da / Num. of mol.: 1 / Fragment: UNP residues 68-332
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhinovirus C / Cell line: transduced HeLa expressing CDHR3 / Cell line (production host): HeLa WisL / Production host: Homo sapiens (human) / References: UniProt: E5D8F2
#4: Protein Capsid protein VP4


Mass: 7174.758 Da / Num. of mol.: 1 / Fragment: UNP residues 2-67
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhinovirus C / Cell line: transduced HeLa expressing CDHR3 / Cell line (production host): HeLa WisL / Production host: Homo sapiens (human) / References: UniProt: E5D8F2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 60 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Rhinovirus C15a / Type: VIRUS
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.
Entity ID: #1-#4 / Source: RECOMBINANT
Molecular weightValue: 8.3 MDa / Experimental value: NO
Source (natural)Organism: Rhinovirus C15a
Source (recombinant)Organism: Homo sapiens (human) / Cell: HeLa / Plasmid: pC15
Details of virusEmpty: NO / Enveloped: NO / Isolate: STRAIN / Type: VIRION
Natural hostOrganism: Homo sapiens
Virus shellName: Capsid (p3) / Diameter: 300 nm / Triangulation number (T number): 3
Buffer solutionpH: 8
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMTrisC4H11NO31
2120 mMsodium chlorideNaCl1
31 mMEDTAC10H16N2O81
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: Ultra thin Lacey carbon
VitrificationInstrument: GATAN CRYOPLUNGE 3 / Cryogen name: ETHANE / Humidity: 80 % / Chamber temperature: 298 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 14000 X / Calibrated defocus min: 700 nm / Calibrated defocus max: 3500 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 14 sec. / Electron dose: 25.7 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 3 / Num. of real images: 8973
Image scansMovie frames/image: 70 / Used frames/image: 3-70

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Processing

EM software
IDNameVersionCategoryDetails
1EMAN22.06particle selectione2boxer.py
2DoG Pickerparticle selection
3Leginon3.1image acquisition
5fitctf2.pyCTF correction
8UCSF Chimera1.11model fitting
10PHENIX1.10.1-2155model refinement
11Coot0.8.2model refinement
12jsprinitial Euler assignment
13jsprfinal Euler assignment
14RELION1.3classification
15jspr3D reconstruction
CTF correctionDetails: CTF correction was performed on the fly during 2D alignment and 3D reconstruction.
Type: PHASE FLIPPING ONLY
Particle selectionNum. of particles selected: 24882
Details: A mixed population of empty particles, full particles, and junk
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 2.79 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 8973 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL / Target criteria: Correlation coefficient

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