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- EMDB-22527: Icosahedral Map of ZIKV MR-766 -

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Basic information

Entry
Database: EMDB / ID: EMD-22527
TitleIcosahedral Map of ZIKV MR-766
Map dataIcosahedral Map of ZIKV MR-766
Sample
  • Virus: Zika virus
Biological speciesZika virus
Methodsingle particle reconstruction / cryo EM / negative staining / Resolution: 3.4 Å
AuthorsJose J / Hafenstein S
CitationJournal: Nat Commun / Year: 2020
Title: Identification of a pocket factor that is critical to Zika virus assembly.
Authors: Nadia M DiNunno / Daniel J Goetschius / Anoop Narayanan / Sydney A Majowicz / Ibrahim Moustafa / Carol M Bator / Susan L Hafenstein / Joyce Jose /
Abstract: Zika virus (ZIKV) is an emerging mosquito borne flavivirus and a major public health concern causing severe disease. Due to the presence of a lipid membrane and structural heterogeneity, attaining an ...Zika virus (ZIKV) is an emerging mosquito borne flavivirus and a major public health concern causing severe disease. Due to the presence of a lipid membrane and structural heterogeneity, attaining an atomic resolution structure is challenging, but important to understand virus assembly and life cycle mechanisms that offer distinct targets for therapeutic intervention. We here use subvolume refinement to achieve a 3.4 Å resolution structure and identify two distinct lipid moieties. The first arises from the inner leaflet and is coordinated by hydrophobic residues of the M and E transmembrane helices that form a binding pocket not previously characterized. The second lipid arises from the outer leaflet coordinate between two E protein helices. Structure-based mutagenesis identifies critical hydrophobic interactions and their effect on the virus life cycle. Results show that lipids play an essential role in the ZIKV assembly pathway revealing a potential target of lipid based antiviral drug development.
History
DepositionAug 31, 2020-
Header (metadata) releaseSep 16, 2020-
Map releaseSep 16, 2020-
UpdateOct 14, 2020-
Current statusOct 14, 2020Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.3
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.3
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_22527.png

Downloads & links

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Map

FileDownload / File: emd_22527.map.gz / Format: CCP4 / Size: 1.1 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationIcosahedral Map of ZIKV MR-766
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 660 pix.
= 726. Å		1.1 Å/pix.
x 660 pix.
= 726. Å		1.1 Å/pix.
x 660 pix.
= 726. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.3 / Movie #1: 0.3
Minimum - Maximum-0.36562908 - 1.2415171
Average (Standard dev.)0.0011413026 (±0.10276404)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions660660660
Spacing660660660
CellA=B=C: 726.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.11.11.1
M x/y/z660660660
origin x/y/z0.0000.0000.000
length x/y/z726.000726.000726.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS660660660
D min/max/mean-0.3661.2420.001

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Supplemental data

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Sample components

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Entire : Zika virus

EntireName: Zika virus
Components
  • Virus: Zika virus

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Supramolecule #1: Zika virus

SupramoleculeName: Zika virus / type: virus / ID: 1 / Parent: 0 / Details: propagated in HeLa cells / NCBI-ID: 64320 / Sci species name: Zika virus / Sci species strain: MR-766 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No
Host (natural)Organism: mosquito (unknown)
Virus shellShell ID: 1 / Name: Zika / Diameter: 50.0 Å / T number (triangulation number): 3

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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

Concentration2 mg/mL
BufferpH: 7
StainingType: NEGATIVE / Material: PTA
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Average electron dose: 41.7 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 9100
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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