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- EMDB-4903: Echovirus 1 intact particle -

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Entry
Database: EMDB / ID: EMD-4903
TitleEchovirus 1 intact particle
Map data
SampleEchovirus E1:
virus / VP1 / VP2 / VP3 / VP4 / ligand
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: 3.5 Å
AuthorsDomanska A / Ruokolainen VP / Pelliccia M / Laajala MA / Marjomaki VS / Butcher SJ
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 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.
#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.
Validation ReportPDB-ID: 6rjf

SummaryFull reportAbout validation report
DateDeposition: Apr 26, 2019 / Header (metadata) release: Jun 12, 2019 / Map release: Jun 12, 2019 / Update: Jun 12, 2019

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Structure visualization

Movie
  • 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-6rjf
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic models: PDB-6rjf
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_4903.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-0.05575123 - 0.12277953
Average (Standard dev.)-0.00021832122 (±0.009797896)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
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
start NX/NY/NZ000
NX/NY/NZ192192192
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS400400400
D min/max/mean-0.0560.123-0.000

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Supplemental data

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Sample components

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Entire Echovirus E1

EntireName: Echovirus E1 / Number of components: 6

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Component #1: virus, Echovirus E1

VirusName: Echovirus E1 / Class: VIRION / 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) / Strain: Human/Egypt/Farouk/1951

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Component #3: protein, VP2

ProteinName: VP2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 28.87226 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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Component #5: protein, VP4

ProteinName: VP4 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 7.398131 kDa
SourceSpecies: Echovirus E1

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Component #6: ligand, PALMITIC ACID

LigandName: PALMITIC ACID / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.256424 kDa

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionBuffer solution: 2 mM magnesium chloride in PBS / 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 acquisition

Image acquisitionNumber of digital images: 979

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: I (icosahedral) / Number of projections: 45309
3D reconstructionSoftware: RELION / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Modeling #1Refinement protocol: rigid body
Input PDB model: 1EV1
Modeling #2Refinement protocol: flexible / Refinement space: REAL
Input PDB model: 1EV1
Modeling #3Refinement protocol: flexible / Refinement space: REAL
Input PDB model: 1EV1
Output model

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