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- EMDB-8396: Asymmetric reconstruction of bacteriophage MS2 mutant NEO1 -

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Basic information

Entry
Database: EMDB / ID: EMD-8396
TitleAsymmetric reconstruction of bacteriophage MS2 mutant NEO1
Map dataCryo-EM reconstruction of mutant NE01 of bacteriophage MS2
Sample
  • Virus: Enterobacterio phage MS2 (virus)
Biological speciesEnterobacterio phage MS2 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 9.5 Å
AuthorsGuerrero-Ferreira RC / Nazarov SY / Zhong Q / Kohn T / Leiman PG
CitationJournal: Environ Sci Technol / Year: 2016
Title: Genetic, Structural, and Phenotypic Properties of MS2 Coliphage with Resistance to ClO Disinfection.
Authors: Qingxia Zhong / Anna Carratalà / Sergey Nazarov / Ricardo Cesar Guerrero-Ferreira / Laura Piccinini / Virginie Bachmann / Petr G Leiman / Tamar Kohn /
Abstract: Common water disinfectants like chlorine have been reported to select for resistant viruses, yet little attention has been devoted to characterizing disinfection resistance. Here, we investigated the ...Common water disinfectants like chlorine have been reported to select for resistant viruses, yet little attention has been devoted to characterizing disinfection resistance. Here, we investigated the resistance of MS2 coliphage to inactivation by chlorine dioxide (ClO). ClO inactivates MS2 by degrading its structural proteins, thereby disrupting the ability of MS2 to attach to and infect its host. ClO-resistant virus populations emerged not only after repeated cycles of ClO disinfection followed by regrowth but also after dilution-regrowth cycles in the absence of ClO. The resistant populations exhibited several fixed mutations which caused the substitution of ClO-labile by ClO-stable amino acids. On a phenotypic level, these mutations resulted in a more stable host binding during inactivation compared to the wild-type, thus resulting in a greater ability to maintain infectivity. This conclusion was supported by cryo-electron microscopy reconstruction of the virus particle, which demonstrated that most structural modification occurred in the putative A protein, an important binding factor. Resistance was specific to the inactivation mechanism of ClO and did not result in significant cross-resistance to genome-damaging disinfectants. Overall, our data indicate that resistant viruses may emerge even in the absence of ClO pressure but that they can be inactivated by other common disinfectants.
History
DepositionSep 12, 2016-
Header (metadata) releaseOct 19, 2016-
Map releaseOct 19, 2016-
UpdateJul 12, 2017-
Current statusJul 12, 2017Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.034
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.034
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_8396.png

Downloads & links

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Map

FileDownload / File: emd_8396.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM reconstruction of mutant NE01 of bacteriophage MS2
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.37 Å/pix.
x 256 pix.
= 350.72 Å		1.37 Å/pix.
x 256 pix.
= 350.72 Å		1.37 Å/pix.
x 256 pix.
= 350.72 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.37 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.034 / Movie #1: 0.034
Minimum - Maximum-0.028017312 - 0.10579934
Average (Standard dev.)0.004356006 (±0.018879531)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 350.72 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.371.371.37
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z350.720350.720350.720
α/β/γ90.00090.00090.000
start NX/NY/NZ00-41
NX/NY/NZ737384
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.0280.1060.004

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Supplemental data

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Sample components

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Entire : Enterobacterio phage MS2

EntireName: Enterobacterio phage MS2 (virus)
Components
  • Virus: Enterobacterio phage MS2 (virus)

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Supramolecule #1: Enterobacterio phage MS2

SupramoleculeName: Enterobacterio phage MS2 / type: virus / ID: 1 / Parent: 0
Details: Wildtype MS2 populations were subjected to repeated propagation without ClO2 exposure. NE01 (non-exposed control 1) is the first of the five resulting populations.
NCBI-ID: 12022 / Sci species name: Enterobacterio phage MS2 / Sci species strain: MS2-NE01 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Escherichia coli (E. coli)
Virus shellShell ID: 1 / T number (triangulation number): 3

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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: 7.4
Details: Phosphate buffered saline: 5 mM Na2HPO4, 10 mM NaCl, pH 7.4
GridModel: Quantifoil / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV
DetailsStock solution concentration: 10E12 pfu/ml.

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Electron microscopy

MicroscopeFEI TECNAI F20
Image recordingFilm or detector model: FEI EAGLE (4k x 4k) / Number real images: 717 / Average exposure time: 1.0 sec. / Average electron dose: 25.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.8 µm
Sample stageSpecimen holder model: GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER
Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 49351
CTF correctionSoftware - Name: CTFFIND (ver. 4)
Startup modelType of model: EMDB MAP
EMDB ID:

1431


Details: Published map was filtered to 60 angstrom and used as initial map
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 9.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 1.4) / Number images used: 22121
Initial angle assignmentType: NOT APPLICABLE / Software - Name: RELION (ver. 1.4)
Final angle assignmentType: NOT APPLICABLE / Software - Name: RELION (ver. 1.4)

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