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

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Basic information

Entry
Database: EMDB / ID: EMD-0565
TitleExtracellular factors prime enterovirus particles for uncoating
Map dataEchovirus 1 expanded particle sharpened map
Sample
  • Virus: Echovirus E1
    • Protein or peptide: VP1
    • Protein or peptide: VP2
    • Protein or peptide: VP3
Keywordsexpanded particle / VIRUS
Function / homology
Function and homology information


caveolin-mediated endocytosis of virus by host cell / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I 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 ...caveolin-mediated endocytosis of virus by host cell / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I 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 / protein complex oligomerization / monoatomic ion channel activity / DNA replication / RNA helicase activity / induction by virus of host autophagy / RNA-directed RNA polymerase / symbiont-mediated suppression of host gene expression / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / host cell nucleus / structural molecule activity / virion attachment to host cell / ATP hydrolysis activity / proteolysis / RNA binding / ATP binding / membrane / metal ion binding
Similarity search - Function
Picornavirus coat protein VP4 superfamily / 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) ...Picornavirus coat protein VP4 superfamily / 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) / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / 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 / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Peptidase S1, PA clan, chymotrypsin-like fold / DNA/RNA polymerase superfamily / Peptidase S1, PA clan / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Biological speciesEchovirus E1
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsDomanska A / Ruokolainen V
Funding support Finland, 4 items
OrganizationGrant numberCountry
Academy of Finland275199 Finland
Academy of Finland315950 Finland
Sigrid Juselius Foundation Finland
Jane and Aatos Erkko Foundation Finland
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 under physiological conditions. Using real-time spectroscopy and sucrose gradients with ...There is limited information about the molecular triggers leading to the uncoating of enteroviruses under physiological conditions. Using real-time spectroscopy and sucrose gradients with radioactively labeled virus, we show at 37°C, the formation 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 the 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 externalized. 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 the uncoating of enteroviruses under 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.
History
DepositionFeb 15, 2019-
Header (metadata) releaseMar 13, 2019-
Map releaseJun 12, 2019-
UpdateMar 20, 2024-
Current statusMar 20, 2024Processing site: RCSB / Status: Released

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Structure visualization

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

emd_0565.png

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)
AnnotationEchovirus 1 expanded particle sharpened map
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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Half map: Echovirus 1 expanded particle half map

Fileemd_0565_half_map_1.map
AnnotationEchovirus 1 expanded particle half map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Echovirus 1 expanded particle half map

Fileemd_0565_half_map_2.map
AnnotationEchovirus 1 expanded particle half map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Echovirus E1

EntireName: Echovirus E1
Components
  • Virus: Echovirus E1
    • Protein or peptide: VP1
    • Protein or peptide: VP2
    • Protein or peptide: VP3

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Supramolecule #1: Echovirus E1

SupramoleculeName: Echovirus E1 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / Details: Echovirus 1 was purified from infected GMK cells / NCBI-ID: 46633 / Sci species name: Echovirus E1 / Virus type: VIRION / Virus isolate: OTHER / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Homo sapiens (human)
Virus shellShell ID: 1 / Name: icosahedral / Diameter: 300.0 Å / T number (triangulation number): 1

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Macromolecule #1: VP1

MacromoleculeName: VP1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Echovirus E1
Molecular weightTheoretical: 31.604373 KDa
SequenceString: GDVQNAVEGA MVRVADTVQT SATNSERVPN LTAVETGHTS QAVPGDTMQT RHVINNHVRS ESTIENFLAR SACVFYLEYK TGTKEDSNS FNNWVITTRR VAQLRRKLEM FTYLRFDMEI TVVITSSQDQ STSQNQNAPV LTHQIMYVPP GGPIPVSVDD Y SWQTSTNP ...String:
GDVQNAVEGA MVRVADTVQT SATNSERVPN LTAVETGHTS QAVPGDTMQT RHVINNHVRS ESTIENFLAR SACVFYLEYK TGTKEDSNS FNNWVITTRR VAQLRRKLEM FTYLRFDMEI TVVITSSQDQ STSQNQNAPV LTHQIMYVPP GGPIPVSVDD Y SWQTSTNP SIFWTEGNAP ARMSIPFISI GNAYSNFYDG WSHFSQAGVY GFTTLNNMGQ LFFRHVNKPN PAAITSVARI YF KPKHVRA WVPRPPRLCP YINSTNVNFE PKPVTEVRTN IITT

UniProtKB: Genome polyprotein

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Macromolecule #2: VP2

MacromoleculeName: VP2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Echovirus E1
Molecular weightTheoretical: 28.126465 KDa
SequenceString: GYSDRVRSIT LGNSTITTQE CANVVVGYGE WPEYLSDNEA TAEDQPTQPD VATCRFYTLD SVQWENGSPG WWWKFPDALR DMGLFGQNM YYHYLGRAGY TIHVQCNASK FHQGCILVVC VPEAEMGSAQ TSGVVNYEHI SKGEIASRFT TTTTAEDHGV Q AAVWNAGM ...String:
GYSDRVRSIT LGNSTITTQE CANVVVGYGE WPEYLSDNEA TAEDQPTQPD VATCRFYTLD SVQWENGSPG WWWKFPDALR DMGLFGQNM YYHYLGRAGY TIHVQCNASK FHQGCILVVC VPEAEMGSAQ TSGVVNYEHI SKGEIASRFT TTTTAEDHGV Q AAVWNAGM GVGVGNLTIF PHQWINLRTN NSATIVMPYV NSVPMDNMYR HHNFTLMIIP FVPLDFSAGA STYVPITVTV AP MCAEYNG LRLAGHQ

UniProtKB: Genome polyprotein

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Macromolecule #3: VP3

MacromoleculeName: VP3 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Echovirus E1
Molecular weightTheoretical: 26.471074 KDa
SequenceString: GLPTMNTPGS NQFLTSDDFQ SPSAMPQFDV TPEMHIPGEV RNLMEIAEVD SVMPINNDSA AKVSSMEAYR VELSTNTNAG TQVFGFQLN PGAESVMNRT LMGEILNYYA HWSGSIKITF VFCGSAMTTG KFLLSYAPPG AGAPKTRKDA MLGTHVVWDV G LQSSCVLC ...String:
GLPTMNTPGS NQFLTSDDFQ SPSAMPQFDV TPEMHIPGEV RNLMEIAEVD SVMPINNDSA AKVSSMEAYR VELSTNTNAG TQVFGFQLN PGAESVMNRT LMGEILNYYA HWSGSIKITF VFCGSAMTTG KFLLSYAPPG AGAPKTRKDA MLGTHVVWDV G LQSSCVLC IPWISQTHYR FVEKDPYTNA GFVTCWYQTS VVSPASNQPK CYMMCMVSAC NDFSVRMLRD TKFIEQTSFY Q

UniProtKB: Genome polyprotein

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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

BufferpH: 7.2
Details: 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
GridModel: Quantifoil R2/2 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Instrument: HOMEMADE PLUNGER

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Sample stageCooling holder cryogen: NITROGEN
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Average exposure time: 47.8 sec. / Average electron dose: 30.0 e/Å2
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2.1)
Final 3D classificationSoftware - Name: RELION (ver. 2.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2.1)
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.1) / Number images used: 14615

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Atomic model buiding 1

Initial modelPDB ID:

4jgy


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-6o06:
Extracellular factors prime enterovirus particles for uncoating

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