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- EMDB-3322: Multiple capsid-stabilizing interactions revealed in a high-resol... -

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Entry
Database: EMDB / ID: EMD-3322
TitleMultiple capsid-stabilizing interactions revealed in a high-resolution structure of an emerging picornavirus causing neonatal sepsis
Map dataAsymmetric reconstruction of human parechovirus 3 (HPeV3).
Sample
  • Sample: Human parechovirus 3 virions
  • Virus: Human parechovirus 3
Keywordsasymmetric reconstruction / HPeV3 / parechovirus / picornavirus / single particle anaylsis / human parechovirus / neonatal sepsis / cryoEM / image processing
Biological speciesHuman parechovirus 3
Methodsingle particle reconstruction / cryo EM / negative staining / Resolution: 10.36 Å
AuthorsShakeel S / Westerhuis BM / Domanska A / Koning RI / Matadeen R / Koster AJ / Bakker AQ / Beaumont T / Wolthers KC / Butcher SJ
CitationJournal: Nat Commun / Year: 2016
Title: Multiple capsid-stabilizing interactions revealed in a high-resolution structure of an emerging picornavirus causing neonatal sepsis.
Authors: Shabih Shakeel / Brenda M Westerhuis / Ausra Domanska / Roman I Koning / Rishi Matadeen / Abraham J Koster / Arjen Q Bakker / Tim Beaumont / Katja C Wolthers / Sarah J Butcher /
Abstract: The poorly studied picornavirus, human parechovirus 3 (HPeV3) causes neonatal sepsis with no therapies available. Our 4.3-Å resolution structure of HPeV3 on its own and at 15 Å resolution in ...The poorly studied picornavirus, human parechovirus 3 (HPeV3) causes neonatal sepsis with no therapies available. Our 4.3-Å resolution structure of HPeV3 on its own and at 15 Å resolution in complex with human monoclonal antibody Fabs demonstrates the expected picornavirus capsid structure with three distinct features. First, 25% of the HPeV3 RNA genome in 60 sites is highly ordered as confirmed by asymmetric reconstruction, and interacts with conserved regions of the capsid proteins VP1 and VP3. Second, the VP0 N terminus stabilizes the capsid inner surface, in contrast to other picornaviruses where on expulsion as VP4, it forms an RNA translocation channel. Last, VP1's hydrophobic pocket, the binding site for the antipicornaviral drug, pleconaril, is blocked and thus inappropriate for antiviral development. Together, these results suggest a direction for development of neutralizing antibodies, antiviral drugs based on targeting the RNA-protein interactions and dissection of virus assembly on the basis of RNA nucleation.
History
DepositionFeb 1, 2016-
Header (metadata) releaseMar 9, 2016-
Map releaseAug 10, 2016-
UpdateAug 24, 2016-
Current statusAug 24, 2016Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.006
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.006
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_3322.tif

Downloads & links

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Map

FileDownload / File: emd_3322.map.gz / Format: CCP4 / Size: 238.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationAsymmetric reconstruction of human parechovirus 3 (HPeV3).
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.14 Å/pix.
x 400 pix.
= 456. Å		1.14 Å/pix.
x 400 pix.
= 456. Å		1.14 Å/pix.
x 400 pix.
= 456. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.14 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.006 / Movie #1: 0.006
Minimum - Maximum-0.01699336 - 0.02527472
Average (Standard dev.)0.00139845 (±0.00581582)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-199-199-199
Dimensions400400400
Spacing400400400
CellA=B=C: 456.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.141.141.14
M x/y/z400400400
origin x/y/z0.0000.0000.000
length x/y/z456.000456.000456.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-199-199-199
NC/NR/NS400400400
D min/max/mean-0.0170.0250.001

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Supplemental data

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Sample components

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Entire : Human parechovirus 3 virions

EntireName: Human parechovirus 3 virions
Components
  • Sample: Human parechovirus 3 virions
  • Virus: Human parechovirus 3

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Supramolecule #1000: Human parechovirus 3 virions

SupramoleculeName: Human parechovirus 3 virions / type: sample / ID: 1000 / Details: The sample was monodisperse / Number unique components: 1

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Supramolecule #1: Human parechovirus 3

SupramoleculeName: Human parechovirus 3 / type: virus / ID: 1 / Name.synonym: HPeV3 / NCBI-ID: 195055 / Sci species name: Human parechovirus 3 / Virus type: VIRION / Virus isolate: OTHER / Virus enveloped: No / Virus empty: No / Syn species name: HPeV3
Host (natural)Organism: Homo sapiens (human) / synonym: VERTEBRATES
Host systemOrganism: Chlorocebus aethiops (grivet) / Recombinant strain: African green monkey / Recombinant cell: Vero
Virus shellShell ID: 1 / Diameter: 280 Å

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Experimental details

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Structure determination

Methodnegative staining, cryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration1 mg/mL
BufferpH: 7.5 / Details: 10mM Tris-HCl, 150mM NaCl, 1mM MgCl2
StainingType: NEGATIVE / Details: unstained sample
GridDetails: Quantifoil holey carbon on copper grids
VitrificationCryogen name: ETHANE / Instrument: LEICA EM GP / Method: Blot for 2 sec on one side before plunging.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
TemperatureMin: 80 K / Max: 95 K / Average: 87 K
Alignment procedureLegacy - Astigmatism: Done as part of Cs corector routine.
DetailsCs corrector was used during imaging.
DateJan 21, 2014
Image recordingCategory: CCD / Film or detector model: FEI FALCON II (4k x 4k) / Number real images: 6604 / Average electron dose: 36 e/Å2
Details: Total number of images used in the reconstruction were 1028.
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 0.01 mm / Nominal defocus max: 2.34 µm / Nominal defocus min: 0.42 µm / Nominal magnification: 59000
Sample stageSpecimen holder: Liquid nitrogen cooled. / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

DetailsThe movie frames were aligned initially by motion_corr. CTF deteremined using CTFFIND3. Particles picked using Ethan. 2D and 3D classification (with icosahedral symmetry imposed) done in Relion. Final reconstruction in Relion.
CTF correctionDetails: Each micrograph
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 10.36 Å / Resolution method: OTHER
Software - Name: Ethan, CTFFIND3, Eman1, Eman2, Auto3DEM, Relion, ResMap
Number images used: 41845
FSC plot (resolution estimation)

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