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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: 8184
TitleCryoEM structure of the native empty particle of a human rhinovirus C
Map dataCryoEM structure of the native empty particle of a human rhinovirus C
SampleRhinovirus C15a:
virus / (Capsid protein ...Capsid) x 3
Function / homologyPeptidase C3, picornavirus core protein 2A / Viral coat protein subunit / Poliovirus 3A protein-like / Helicase, superfamily 3, single-stranded RNA virus / Peptidase S1, PA clan / RNA-directed RNA polymerase, catalytic domain / Picornavirus coat protein VP4 / Picornavirus 2B protein / Picornavirus capsid / RNA-directed RNA polymerase, C-terminal domain ...Peptidase C3, picornavirus core protein 2A / Viral coat protein subunit / Poliovirus 3A protein-like / Helicase, superfamily 3, single-stranded RNA virus / Peptidase S1, PA clan / RNA-directed RNA polymerase, catalytic domain / Picornavirus coat protein VP4 / Picornavirus 2B protein / Picornavirus capsid / RNA-directed RNA polymerase, C-terminal domain / Helicase, superfamily 3, single-stranded DNA/RNA virus / Peptidase C3A/C3B, picornaviral / Picornavirus/Calicivirus coat protein / Poliovirus core protein 3a, soluble domain / Picornavirus coat protein VP4 superfamily / picornavirus capsid protein / RNA dependent RNA polymerase / Superfamily 3 helicase of positive ssRNA viruses domain profile. / RdRp of positive ssRNA viruses catalytic domain profile. / Poliovirus 3A protein like / Picornavirus coat protein (VP4) / Picornavirus 2B protein / Picornavirus core protein 2A / RNA helicase / P-loop containing nucleoside triphosphate hydrolase / 3C cysteine protease (picornain 3C) / picornain 2A / pore-mediated entry of viral genome into host cell / suppression by virus of host mRNA export from nucleus / suppression by virus of host RIG-I activity / picornain 3C / T=pseudo3 icosahedral viral capsid / endocytosis involved in viral entry into host cell / RNA-protein covalent cross-linking / host cell cytoplasmic vesicle membrane / pore formation by virus in membrane of host cell / integral to membrane of host cell / RNA helicase activity / nucleoside-triphosphate phosphatase / RNA-directed RNA polymerase / suppression by virus of host gene expression / induction by virus of host autophagy / ion channel activity / protein complex oligomerization / viral RNA genome replication / RNA-directed 5'-3' RNA polymerase activity / cysteine-type endopeptidase activity / transcription, DNA-templated / virion attachment to host cell / structural molecule activity / RNA binding / membrane / ATP binding / Genome polyprotein
Function and homology information
SourceRhinovirus C15a / Rhinovirus C
Methodsingle particle reconstruction / cryo EM / 3.16 Å resolution
AuthorsLiu Y / Hill MG / Klose T / Chen Z / Watters KE / Jiang W / Palmenberg AC / Rossmann MG
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
Validation ReportPDB-ID: 5jzg

SummaryFull reportAbout validation report
DateDeposition: May 16, 2016 / Header (metadata) release: Jun 8, 2016 / Map release: Jul 13, 2016 / Last update: Jul 18, 2018

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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 models: PDB-5jzg
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_8184.map.gz (map file in CCP4 format, 442369 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
480 pix
1.04 Å/pix.
= 499.2 Å
480 pix
1.04 Å/pix.
= 499.2 Å
480 pix
1.04 Å/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 Level:13.4 (by author), 13.4 (movie #1):
Minimum - Maximum-48.974299999999999 - 67.214264
Average (Standard dev.)0.06435112 (3.4875524)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions480480480
Origin0.0.0.
Limit479.479.479.
Spacing480480480
CellA=B=C: 499.19998 Å
α=β=γ: 90.0 deg.

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
start NX/NY/NZ
NX/NY/NZ
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 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 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. 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 reconstructionCTF 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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