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- EMDB-8184: CryoEM structure of the native empty particle of a human rhinovirus C -

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Basic information

Entry
Database: EMDB / ID: EMD-8184
TitleCryoEM structure of the native empty particle of a human rhinovirus C
Map data
SampleRhinovirus C15a:
virus / (Capsid protein ...Capsid) x 3
Function / homology
Function and homology information


suppression by virus of host innate immune response / picornain 2A / pore-mediated entry of viral genome into host cell / suppression by virus of host mRNA export from nucleus / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / RNA-protein covalent cross-linking / integral to membrane of host cell / pore formation by virus in membrane of host cell ...suppression by virus of host innate immune response / picornain 2A / pore-mediated entry of viral genome into host cell / suppression by virus of host mRNA export from nucleus / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / RNA-protein covalent cross-linking / integral to membrane of host cell / pore formation by virus in membrane of host cell / endocytosis involved in viral entry into host cell / protein complex oligomerization / cytoplasmic vesicle membrane / nucleoside-triphosphate phosphatase / ion channel activity / suppression by virus of host gene expression / induction by virus of host autophagy / RNA-directed RNA polymerase / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed 5'-3' RNA polymerase activity / RNA helicase activity / transcription, DNA-templated / virion attachment to host cell / host cell nucleus / structural molecule activity / RNA binding / ATP binding / metal ion binding
RNA-directed RNA polymerase, catalytic domain / Poliovirus 3A protein-like / P-loop containing nucleoside triphosphate hydrolase / Peptidase C3, picornavirus core protein 2A / Peptidase S1, PA clan / Peptidase C3A/C3B, picornaviral / Helicase, superfamily 3, single-stranded DNA/RNA virus / RNA-directed RNA polymerase, C-terminal domain / Viral coat protein subunit / Picornavirus capsid ...RNA-directed RNA polymerase, catalytic domain / Poliovirus 3A protein-like / P-loop containing nucleoside triphosphate hydrolase / Peptidase C3, picornavirus core protein 2A / Peptidase S1, PA clan / Peptidase C3A/C3B, picornaviral / Helicase, superfamily 3, single-stranded DNA/RNA virus / RNA-directed RNA polymerase, C-terminal domain / Viral coat protein subunit / Picornavirus capsid / Picornavirus/Calicivirus coat protein / Poliovirus core protein 3a, soluble domain / Picornavirus 2B protein / Picornavirus coat protein VP4 superfamily / Reverse transcriptase/Diguanylate cyclase domain / DNA/RNA polymerase superfamily / Peptidase S1, PA clan, chymotrypsin-like fold / Picornavirales 3C/3C-like protease domain / Picornavirus coat protein VP4 / Helicase, superfamily 3, single-stranded RNA virus
Genome polyprotein
Biological speciesRhinovirus C15a / Rhinovirus C
Methodsingle particle reconstruction / cryo EM / Resolution: 3.16 Å
AuthorsLiu Y / Hill MG / Klose T / Chen Z / Watters KE / Jiang W / Palmenberg AC / Rossmann MG
Funding support United States, 2 items
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.
Validation ReportSummary, Full report, XML, About validation report
History
DepositionMay 16, 2016-
Header (metadata) releaseJun 8, 2016-
Map releaseJul 13, 2016-
UpdateDec 11, 2019-
Current statusDec 11, 2019Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 13.4
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 13.4
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5jzg
  • Surface level: 13.4
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-5jzg
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_8184.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.04 Å/pix.
x 480 pix.
= 499.2 Å
1.04 Å/pix.
x 480 pix.
= 499.2 Å
1.04 Å/pix.
x 480 pix.
= 499.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.04 Å
Density
Contour LevelBy AUTHOR: 13.4 / Movie #1: 13.4
Minimum - Maximum-48.9743 - 67.214264
Average (Standard dev.)0.06435112 (±3.4875524)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 499.19998 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.041.041.04
M x/y/z480480480
origin x/y/z0.0000.0000.000
length x/y/z499.200499.200499.200
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS480480480
D min/max/mean-48.97467.2140.064

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Supplemental data

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Sample components

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Entire Rhinovirus C15a

EntireName: 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

VirusName: 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
MassTheoretical: 5.8 MDa
SpeciesSpecies: Rhinovirus C15a
Source (engineered)Expression System: Homo sapiens (human) / Vector: pC15 / Cell of expression system: HeLa
Source (natural)Host Species: Homo sapiens (human)
Shell #1Name of element: Capsid (p3) / Diameter: 300.0 Å / T number (triangulation number): 3

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Component #2: protein, Capsid protein VP1

ProteinName: Capsid protein VP1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 31.802623 kDa
SourceSpecies: Rhinovirus C
Source (engineered)Expression System: Homo sapiens (human)

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Component #3: protein, Capsid protein VP3

ProteinName: Capsid protein VP3 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 25.965037 kDa
SourceSpecies: Rhinovirus C
Source (engineered)Expression System: Homo sapiens (human)

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Component #4: protein, Capsid protein VP0

ProteinName: Capsid protein VP0 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 36.247344 kDa
SourceSpecies: Rhinovirus C
Source (engineered)Expression System: Homo sapiens (human)

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionSpecimen conc.: 1 mg/mL / pH: 8
VitrificationInstrument: GATAN CRYOPLUNGE 3 / Cryogen name: ETHANE / Temperature: 298 K / Humidity: 80 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 25.7 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 14000.0 X (nominal) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 3614

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: I (icosahedral) / Number of projections: 3614
3D reconstructionSoftware: 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 #1Refinement protocol: rigid body / Target criteria: Correlation coefficient / Refinement space: REAL
Output model

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