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- EMDB-2390: The limits of structural plasticity in a picornavirus capsid reve... -

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Basic information

Entry
Database: EMDB / ID: EMD-2390
TitleThe limits of structural plasticity in a picornavirus capsid revealed by a massively expanded equine rhinitis A virus particle
Map dataReconstruction of expanded equine rhinitis A virus
Sample
  • Sample: expanded equine rhinitis A virus
  • Virus: Equine rhinitis A virus
Keywordsvirus / picornavirus / capsid structure / capsid expansion / uncoating
Function / homology
Function and homology information


icosahedral viral capsid / host cell cytoplasm / symbiont entry into host cell / structural molecule activity / virion attachment to host cell / cytoplasm
Similarity search - Function
Capsid protein VP4, Picornavirus / Viral protein VP4 subunit / Capsid protein VP4 superfamily, Picornavirus / Picornavirus capsid / picornavirus capsid protein / Picornavirus/Calicivirus coat protein / Viral coat protein subunit
Similarity search - Domain/homology
Genome polyprotein / Genome polyprotein / Genome polyprotein
Similarity search - Component
Biological speciesEquine rhinitis A virus
Methodsingle particle reconstruction / cryo EM / Resolution: 17.0 Å
AuthorsBakker SE / Groppelli E / Pearson AR / Stockley PG / Rowlands DJ / Ranson NA
CitationJournal: J Virol / Year: 2014
Title: Limits of structural plasticity in a picornavirus capsid revealed by a massively expanded equine rhinitis A virus particle.
Authors: Saskia E Bakker / Elisabetta Groppelli / Arwen R Pearson / Peter G Stockley / David J Rowlands / Neil A Ranson /
Abstract: The Picornaviridae family of small, nonenveloped viruses includes major pathogens of humans and animals. They have positive-sense, single-stranded RNA genomes, and the mechanism(s) by which these ...The Picornaviridae family of small, nonenveloped viruses includes major pathogens of humans and animals. They have positive-sense, single-stranded RNA genomes, and the mechanism(s) by which these genomes are introduced into cells to initiate infection remains poorly understood. The structures of presumed uncoating intermediate particles of several picornaviruses show limited expansion and some increased porosity compared to the mature virions. Here, we present the cryo-electron microscopy structure of native equine rhinitis A virus (ERAV), together with the structure of a massively expanded ERAV particle, each at ∼17-Å resolution. The expanded structure has large pores on the particle 3-fold axes and has lost the RNA genome and the capsid protein VP4. The expanded structure thus illustrates both the limits of structural plasticity in such capsids and a plausible route by which genomic RNA might exit.
IMPORTANCE: Picornaviruses are important animal and human pathogens that protect their genomic RNAs within a protective protein capsid. Upon infection, this genomic RNA must be able to leave the ...IMPORTANCE: Picornaviruses are important animal and human pathogens that protect their genomic RNAs within a protective protein capsid. Upon infection, this genomic RNA must be able to leave the capsid to initiate a new round of infection. We describe here the structure of a unique, massively expanded state of equine rhinitis A virus that provides insight into how this exit might occur.
History
DepositionMay 30, 2013-
Header (metadata) releaseJul 3, 2013-
Map releaseApr 2, 2014-
UpdateMay 28, 2014-
Current statusMay 28, 2014Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 1
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-4ctg
  • Surface level: 1
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-4ctg
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_2390.png

Downloads & links

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Map

FileDownload / File: emd_2390.map.gz / Format: CCP4 / Size: 51.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of expanded equine rhinitis A virus
Voxel sizeX=Y=Z: 1.72 Å
Density
Contour LevelBy AUTHOR: 1.0 / Movie #1: 1
Minimum - Maximum-3.30300045 - 5.0
Average (Standard dev.)0.00326529 (±0.98152566)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 412.80002 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.721.721.72
M x/y/z240240240
origin x/y/z0.0000.0000.000
length x/y/z412.800412.800412.800
α/β/γ90.00090.00090.000
start NX/NY/NZ00-40
NX/NY/NZ555581
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS240240240
D min/max/mean-3.3035.0000.003

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Supplemental data

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Sample components

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Entire : expanded equine rhinitis A virus

EntireName: expanded equine rhinitis A virus
Components
  • Sample: expanded equine rhinitis A virus
  • Virus: Equine rhinitis A virus

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Supramolecule #1000: expanded equine rhinitis A virus

SupramoleculeName: expanded equine rhinitis A virus / type: sample / ID: 1000 / Oligomeric state: One icosahedral virus particle / Number unique components: 1

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Supramolecule #1: Equine rhinitis A virus

SupramoleculeName: Equine rhinitis A virus / type: virus / ID: 1 / Name.synonym: ERAV / NCBI-ID: 47000 / Sci species name: Equine rhinitis A virus / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: Yes / Syn species name: ERAV
Host (natural)Organism: Equus caballus (horse) / synonym: VERTEBRATES
Host systemOrganism: Homo sapiens (human) / Recombinant cell: HeLa cells
Virus shellShell ID: 1 / Diameter: 316 Å

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration2 mg/mL
GridDetails: 300 mesh quantifoil R1.2/1.3 grids, glow discharged in air.
VitrificationCryogen name: ETHANE / Instrument: HOMEMADE PLUNGER

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Electron microscopy

MicroscopeFEI TECNAI F20
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 87209 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2 mm
Sample stageSpecimen holder: 626 / Specimen holder model: GATAN LIQUID NITROGEN
DateJan 1, 2011
Image recordingCategory: CCD / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Average electron dose: 15 e/Å2
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: phase flipping, each particle
Final two d classificationNumber classes: 78
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 17.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: SPIDER / Number images used: 227

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Atomic model buiding 1

Initial modelPDB ID:

1asj

SoftwareName: Chimera
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-4ctg:
The limits of structural plasticity in a picornavirus capsid revealed by a massively expanded equine rhinitis A virus particle

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