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- EMDB-0565: Extracellular factors prime enterovirus particles for uncoating -

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Entry
Database: EMDB / ID: EMD-0565
TitleExtracellular factors prime enterovirus particles for uncoating
Map data
SampleEchovirus E1:
virus / VP1 / VP2 / VP3
Function / homology
Function and homology information


caveolin-mediated endocytosis of virus by host cell / suppression by virus of host translation initiation factor activity / positive stranded viral RNA replication / ec:3.4.22.29: / 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 / ec:3.4.22.28: / RNA-protein covalent cross-linking / T=pseudo3 icosahedral viral capsid ...caveolin-mediated endocytosis of virus by host cell / suppression by virus of host translation initiation factor activity / positive stranded viral RNA replication / ec:3.4.22.29: / 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 / ec:3.4.22.28: / RNA-protein covalent cross-linking / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / pore formation by virus in membrane of host cell / integral to membrane of host cell / RNA helicase activity / ec:3.6.1.15: / suppression by virus of host gene expression / ec:2.7.7.48: / induction by virus of host autophagy / ion channel activity / protein complex oligomerization / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-directed 5'-3' RNA polymerase activity / DNA replication / transcription, DNA-templated / virion attachment to host cell / structural molecule activity / RNA binding / membrane / ATP binding
Viral coat protein subunit / 3C cysteine protease (picornain 3C) / Peptidase C3A/C3B, picornaviral / Helicase, superfamily 3, single-stranded DNA/RNA virus / RNA-directed RNA polymerase, C-terminal domain / Picornavirus coat protein VP4 superfamily / Picornavirus/Calicivirus coat protein / Picornavirus capsid / Picornavirus 2B protein / Picornavirus coat protein VP4 ...Viral coat protein subunit / 3C cysteine protease (picornain 3C) / Peptidase C3A/C3B, picornaviral / Helicase, superfamily 3, single-stranded DNA/RNA virus / RNA-directed RNA polymerase, C-terminal domain / Picornavirus coat protein VP4 superfamily / Picornavirus/Calicivirus coat protein / Picornavirus capsid / Picornavirus 2B protein / Picornavirus coat protein VP4 / AAA+ ATPase domain / RNA-directed RNA polymerase, catalytic domain / picornavirus capsid protein / Peptidase S1, PA clan / Poliovirus core protein 3a, soluble domain / RNA dependent RNA polymerase / RNA helicase / Picornavirus core protein 2A / Picornavirus 2B protein / Picornavirus coat protein (VP4) / Poliovirus 3A protein like / RdRp of positive ssRNA viruses catalytic domain profile. / Superfamily 3 helicase of positive ssRNA viruses domain profile. / Helicase, superfamily 3, single-stranded RNA virus / Picornavirales 3C/3C-like protease domain profile. / Poliovirus 3A protein-like / P-loop containing nucleoside triphosphate hydrolase / Peptidase C3, picornavirus core protein 2A
Genome polyprotein
Biological speciesEchovirus E1 / E-1 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsDomanska A / Ruokolainen V / Pelliccia M / Laajala M / Butcher SJ / Marjomaki VS
CitationJournal: J. Virol. / Year: 2019
Title: Extracellular albumin and endosomal ions prime enterovirus particles for uncoating that can be prevented by fatty acid saturation.
Authors: Visa Ruokolainen / Aušra Domanska / Mira Laajala / Maria Pelliccia / Sarah J Butcher / Varpu Marjomäki /
Abstract: There is limited information about the molecular triggers leading to the uncoating of enteroviruses in physiological conditions. Using real-time spectroscopy and sucrose gradients with ...There is limited information about the molecular triggers leading to the uncoating of enteroviruses in physiological conditions. Using real-time spectroscopy and sucrose gradients with radioactively-labeled virus we show at 37 °C, formation of a low amount of albumin-triggered, metastable, uncoating intermediate of echovirus 1 without receptor engagement. This conversion was blocked by saturating the albumin with fatty acids. High potassium but low sodium and calcium concentrations, mimicking the endosomal environment, also induced the formation of a metastable uncoating intermediate of echovirus 1. Together, these factors boosted the formation of the uncoating intermediate and infectivity of this intermediate was retained, as judged by end-point titration. Cryo-electron microscopy reconstruction of the virions treated with albumin and high potassium, low sodium and low calcium concentrations resulted in a 3.6 Å resolution model revealing a fenestrated capsid showing 4 % expansion and loss of the pocket factor, similarly to altered (A-) particles described for other enteroviruses. The dimer interface between VP2 molecules was opened, the VP1 N-termini disordered and most likely externalised. The RNA was clearly visible, anchored to the capsid. The results presented here suggest that extracellular albumin, partially saturated with fatty acids, likely leads to the formation of the infectious uncoating intermediate prior to the engagement with the cellular receptor. In addition, changes in mono- and divalent cations, likely occurring in endosomes, promote capsid opening and genome release.There is limited information about uncoating of enteroviruses in physiological conditions. Here, we focused on physiologically relevant factors that likely contribute to opening of echovirus 1 and other B-group enteroviruses. By combining biochemical and structural data, we show, that before entering cells, extracellular albumin is capable of priming the virus into a metastable, yet infectious intermediate state. The ionic changes that are suggested to occur in endosomes, can further contribute to uncoating and promote genome release, once the viral particle is endocytosed. Importantly, we provide a detailed high-resolution structure of a virion after treatment with albumin and a preset ion composition, showing pocket factor release, capsid expansion and fenestration, and the clearly visible genome still anchored to the capsid. This study provides valuable information about the physiological factors that contribute to the opening of B-group enteroviruses.
Validation ReportPDB-ID: 6o06

SummaryFull reportAbout validation report
DateDeposition: Feb 15, 2019 / Header (metadata) release: Mar 13, 2019 / Map release: Jun 12, 2019 / Update: Jun 12, 2019

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Structure visualization

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  • Surface view with section colored by density value
  • Surface level: 0.02
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  • Surface view colored by radius
  • Surface level: 0.02
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  • Surface view with fitted model
  • Atomic models: : PDB-6o06
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic models: PDB-6o06
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Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_0565.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.24 Å/pix.
x 400 pix.
= 496. Å
1.24 Å/pix.
x 400 pix.
= 496. Å
1.24 Å/pix.
x 400 pix.
= 496. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.24 Å
Density
Contour LevelBy AUTHOR: 0.02 / Movie #1: 0.02
Minimum - Maximum-0.07406282 - 0.16077633
Average (Standard dev.)0.0016680729 (±0.011457966)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-200-200-200
Dimensions400400400
Spacing400400400
CellA=B=C: 496.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.241.241.24
M x/y/z400400400
origin x/y/z0.0000.0000.000
length x/y/z496.000496.000496.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-200-200-200
NC/NR/NS400400400
D min/max/mean-0.0740.1610.002

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Supplemental data

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Sample components

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Entire Echovirus E1

EntireName: Echovirus E1 / Details: Echovirus 1 was purified from infected GMK cells / Number of components: 4

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Component #1: virus, Echovirus E1

VirusName: Echovirus E1 / Class: VIRION / Details: Echovirus 1 was purified from infected GMK cells / Empty: No / Enveloped: No / Isolate: OTHER
SpeciesSpecies: Echovirus E1
Source (natural)Host Species: Homo sapiens (human)
Shell #1Name of element: icosahedral / Diameter: 300.0 Å / T number (triangulation number): 1

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Component #2: protein, VP1

ProteinName: VP1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 31.604373 kDa
SourceSpecies: E-1 (virus)

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Component #3: protein, VP2

ProteinName: VP2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 28.126465 kDa
SourceSpecies: E-1 (virus)

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Component #4: protein, VP3

ProteinName: VP3 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 26.471074 kDa
SourceSpecies: E-1 (virus)

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionBuffer solution: 29 mM sodium chloride, 28 mM potassium ion, 0.145 mM magnesium chloride, 8 mM phosphate dibasic, 2 mM phosphate monobasic, 0.0093% faf-BSA
pH: 7.2
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
ImagingMicroscope: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 30 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: FEI FALCON III (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: I (icosahedral) / Number of projections: 14615
3D reconstructionSoftware: RELION / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Modeling #1Refinement protocol: flexible / Refinement space: REAL
Input PDB model: 4JGY
Output model

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