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- PDB-6rjf: Echovirus 1 intact particle -

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Basic information

Entry
Database: PDB / ID: 6rjf
TitleEchovirus 1 intact particle
Components
  • VP1
  • VP2
  • VP3
  • VP4
KeywordsVIRUS / VIRAL COAT PROTEIN / CAPSID / PICORNAVIRUS / ECHOVIRUS / ICOSAHEDRAL 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 / : / viral capsid ...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 / : / viral capsid / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / host cell cytoplasm / 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 / cytoplasm
Similarity search - Function
Jelly Rolls - #20 / 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 ...Jelly Rolls - #20 / 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 / Jelly Rolls / 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 / Sandwich / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
PALMITIC ACID / Capsid protein VP0 / Genome polyprotein
Similarity search - Component
Biological speciesEchovirus E1
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsDomanska, A. / Ruokolainen, V.P. / Pelliccia, M. / Laajala, M.A. / Marjomaki, V.S. / Butcher, S.J.
Funding support Finland, 4items
OrganizationGrant numberCountry
Academy of Finland275199 Finland
Academy of Finland315950 Finland
Sigrid Juselius Foundation Finland
Jane and Aatos Erkko Foundation Finland
Citation
Journal: 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.
#1: Journal: Acta Crystallogr D Biol Crystallogr / Year: 1998
Title: Structure determination of echovirus 1.
Authors: D J Filman / M W Wien / J A Cunningham / J M Bergelson / J M Hogle /
Abstract: The atomic structure of echovirus 1 (a member of the enterovirus genus of the picornavirus family) has been determined using cryo-crystallography and refined to 3.55 A resolution. Echovirus 1 ...The atomic structure of echovirus 1 (a member of the enterovirus genus of the picornavirus family) has been determined using cryo-crystallography and refined to 3.55 A resolution. Echovirus 1 crystallizes in space group P22121 with a = 352.45, b = 472.15 and c = 483.20 A. The crystals contain one full virus particle in the asymmetric unit allowing for 60-fold noncrystallographic symmetry averaging. The diffraction pattern shows strong pseudo-B-centering with reflections with h + l = 2n + 1 being systematically weak or absent below about 6 A resolution. The size of the unit cell and presence of pseudo-B-centering placed strong constraints on the allowed packing of the icosahedral particle in the crystal lattice. These constraints greatly facilitated the determination of the orientation and position of the virus by reducing the dimensionality of the search, but interactions between the crystallographic and noncrystallographic symmetries rendered the choice of space group ambiguous until very late in the structure determination. This structure determination provides a striking example of the power of packing analysis in molecular replacement and illustrates how subtle interactions between crystallographic and noncrystallographic symmetries can be resolved.
#2: Journal: Acta Crystallogr D Biol Crystallogr / Year: 1996
Title: A pseudo-cell based approach to efficient crystallographic refinement of viruses.
Authors: D H Jacobson / J M Hogle / D J Filman /
Abstract: Strategies have been developed for the inexpensive refinement of atomic models of viruses and of other highly symmetric structures. These methods, which have been used in the refinement of several ...Strategies have been developed for the inexpensive refinement of atomic models of viruses and of other highly symmetric structures. These methods, which have been used in the refinement of several strains of poliovirus, focus on an arbitrary-sized parallelepiped (termed the 'protomer' box) containing a single complete averaged copy of the structural motif which forms the protein capsid, together with the fragments of other symmetry-related copies of the motif which are located in its immediate neighborhood. The Fourier transform of the protomer box provides reference structure factors for stereochemically restrained crystallographic refinement of the atomic model parameters. The phases of the reference structure factors are based on the averaged map, and are not permitted to change during the refinement. It is demonstrated that models refined using the protomer box methods do not differ significantly from models refined by more expensive full-cell calculations.
History
DepositionApr 26, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 12, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2019Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / em_admin / pdbx_database_proc
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name / _em_admin.last_update
Revision 1.2Aug 21, 2019Group: Data collection / Database references / Category: citation / citation_author / em_image_scans
Item: _citation.journal_volume / _citation.title / _citation_author.identifier_ORCID

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Assembly

Deposited unit
1: VP1
2: VP2
3: VP3
4: VP4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,6025
Polymers94,3464
Non-polymers2561
Water0
1
1: VP1
2: VP2
3: VP3
4: VP4
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)5,676,136300
Polymers5,660,750240
Non-polymers15,38560
Water0
TypeNameSymmetry operationNumber
point symmetry operation60
Buried area21690 Å2
ΔGint-107 kcal/mol
Surface area34740 Å2
MethodPISA

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Components

#1: Protein VP1


Mass: 31604.373 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Echovirus E1 / Strain: Human/Egypt/Farouk/1951 / References: UniProt: O91734
#2: Protein VP2


Mass: 28872.260 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Echovirus E1 / References: UniProt: O91734
#3: Protein VP3


Mass: 26471.074 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Echovirus E1 / References: UniProt: O91734
#4: Protein VP4


Mass: 7398.131 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Echovirus E1 / References: UniProt: C4B607*PLUS
#5: Chemical ChemComp-PLM / PALMITIC ACID / Palmitic acid


Mass: 256.424 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H32O2

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Echovirus E1 / Type: VIRUS / Entity ID: #1-#4 / Source: NATURAL
Molecular weightUnits: MEGADALTONS / Experimental value: NO
Source (natural)Organism: Echovirus E1
Details of virusEmpty: NO / Enveloped: NO / Isolate: OTHER / Type: VIRION
Natural hostOrganism: Homo sapiens
Virus shellName: icosahedralIcosahedron / Diameter: 300 nm / Triangulation number (T number): 1
Buffer solutionpH: 7.2 / Details: 2 mM magnesium chloride in PBS
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid type: Quantifoil R2/2
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 30 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k) / Num. of real images: 979

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Processing

EM software
IDNameVersionCategoryFitting-ID
1RELION2.1particle selection
3EPUimage acquisition
5GctfCTF correction
8UCSF Chimeramodel fitting1
10Coot0.8.8model refinement1
14Coot0.8.9.1model refinement2
16MDFFmodel refinement3
17RELION2.1initial Euler assignment
19RELION2.1final Euler assignment
21RELION2.1classification
23RELION2.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 45309
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 45309 / Symmetry type: POINT
Atomic model building
IDProtocolSpace
1RIGID BODY FIT
2FLEXIBLE FITREAL
3FLEXIBLE FITREAL
Atomic model building
IDPDB-ID 3D fitting-ID
11EV1

1ev1

1
21EV1

1ev1

2
31EV1

1ev1

3

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