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- EMDB-22339: The cryo-EM map of Aureococcus anophagefferens Virus (AaV) -

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Basic information

Entry
Database: EMDB / ID: EMD-22339
TitleThe cryo-EM map of Aureococcus anophagefferens Virus (AaV)
Map dataMap of the capsid of Aureococcus anophagefferens Virus
Sample
  • Virus: Aureococcus anophagefferens virus
Biological speciesAureococcus anophagefferens virus
Methodsingle particle reconstruction / cryo EM / Resolution: 9.5 Å
AuthorsGann ER / Xian Y / Abraham PE / Hettich RL / Reynolds TB / Xiao C / Wilhelm SW
CitationJournal: Front Microbiol / Year: 2020
Title: Structural and Proteomic Studies of the Virus Demonstrate a Global Distribution of Virus-Encoded Carbohydrate Processing.
Authors: Eric R Gann / Yuejiao Xian / Paul E Abraham / Robert L Hettich / Todd B Reynolds / Chuan Xiao / Steven W Wilhelm /
Abstract: Viruses modulate the function(s) of environmentally relevant microbial populations, yet considerations of the metabolic capabilities of individual virus particles themselves are rare. We used shotgun ...Viruses modulate the function(s) of environmentally relevant microbial populations, yet considerations of the metabolic capabilities of individual virus particles themselves are rare. We used shotgun proteomics to quantitatively identify 43 virus-encoded proteins packaged within purified Virus (AaV) particles, normalizing data to the per-virion level using a 9.5-Å-resolution molecular reconstruction of the 1900-Å (AaV) particle that we generated with cryogenic electron microscopy. This packaged proteome was used to determine similarities and differences between members of different giant virus families. We noted that proteins involved in sugar degradation and binding (e.g., carbohydrate lyases) were unique to AaV among characterized giant viruses. To determine the extent to which this virally encoded metabolic capability was ecologically relevant, we examined the TARA Oceans dataset and identified genes and transcripts of viral origin. Our analyses demonstrated that putative giant virus carbohydrate lyases represented up to 17% of the marine pool for this function. In total, our observations suggest that the AaV particle has potential prepackaged metabolic capabilities and that these may be found in other giant viruses that are widespread and abundant in global oceans.
History
DepositionJul 21, 2020-
Header (metadata) releaseSep 30, 2020-
Map releaseSep 30, 2020-
UpdateOct 21, 2020-
Current statusOct 21, 2020Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0168
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.0168
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.0168
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_22339.png

Downloads & links

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Map

FileDownload / File: emd_22339.map.gz / Format: CCP4 / Size: 4 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMap of the capsid of Aureococcus anophagefferens Virus
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.68 Å/pix.
x 1024 pix.
= 2744.32 Å		2.68 Å/pix.
x 1024 pix.
= 2744.32 Å		2.68 Å/pix.
x 1024 pix.
= 2744.32 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.68 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0168 / Movie #1: 0.0168
Minimum - Maximum-0.0059061274 - 0.03415135
Average (Standard dev.)0.00027662326 (±0.002022592)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions102410241024
Spacing102410241024
CellA=B=C: 2744.32 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.682.682.68
M x/y/z102410241024
origin x/y/z0.0000.0000.000
length x/y/z2744.3202744.3202744.320
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ304304304
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS102410241024
D min/max/mean-0.0060.0340.000

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Supplemental data

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Sample components

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Entire : Aureococcus anophagefferens virus

EntireName: Aureococcus anophagefferens virus
Components
  • Virus: Aureococcus anophagefferens virus

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Supramolecule #1: Aureococcus anophagefferens virus

SupramoleculeName: Aureococcus anophagefferens virus / type: virus / ID: 1 / Parent: 0 / NCBI-ID: 1474867 / Sci species name: Aureococcus anophagefferens virus / Virus type: VIRION / Virus isolate: OTHER / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Aureococcus anophagefferens (eukaryote)
Virus shellShell ID: 1 / Diameter: 1900.0 Å / T number (triangulation number): 169

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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: 8
Details: 50 mM Tris base, 250 mM sodium chloride, 5 mM magnesium chloride
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 30.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated defocus max: 6.842 µm / Calibrated defocus min: 0.493 µm / Calibrated magnification: 105000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 9.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 570
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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