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- EMDB-0451: Enterobacteria phage MS2 -

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Basic information

Entry
Database: EMDB / ID: EMD-0451
TitleEnterobacteria phage MS2
Map dataEnterobacteria phage MS2
Sample
  • Virus: Enterobacteria phage MS2 (virus)
Biological speciesEnterobacteria phage MS2 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.7 Å
AuthorsMeng R / Cui Z / Zhang J
CitationJournal: Nat Commun / Year: 2019
Title: Structural basis for the adsorption of a single-stranded RNA bacteriophage.
Authors: Ran Meng / Mengqiu Jiang / Zhicheng Cui / Jeng-Yih Chang / Kailu Yang / Joanita Jakana / Xinzhe Yu / Zhao Wang / Bo Hu / Junjie Zhang /
Abstract: Single-stranded RNA bacteriophages (ssRNA phages) infect Gram-negative bacteria via a single maturation protein (Mat), which attaches to a retractile pilus of the host. Here we present structures of ...Single-stranded RNA bacteriophages (ssRNA phages) infect Gram-negative bacteria via a single maturation protein (Mat), which attaches to a retractile pilus of the host. Here we present structures of the ssRNA phage MS2 in complex with the Escherichia coli F-pilus, showing a network of hydrophobic and electrostatic interactions at the Mat-pilus interface. Moreover, binding of the pilus induces slight orientational variations of the Mat relative to the rest of the phage capsid, priming the Mat-connected genomic RNA (gRNA) for its release from the virions. The exposed tip of the attached Mat points opposite to the direction of the pilus retraction, which may facilitate the translocation of the gRNA from the capsid into the host cytosol. In addition, our structures determine the orientation of the assembled F-pilin subunits relative to the cell envelope, providing insights into the F-like type IV secretion systems.
History
DepositionJan 10, 2019-
Header (metadata) releaseFeb 6, 2019-
Map releaseJul 24, 2019-
UpdateJul 31, 2019-
Current statusJul 31, 2019Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.035
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.035
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0451.png

Downloads & links

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Map

FileDownload / File: emd_0451.map.gz / Format: CCP4 / Size: 15.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationEnterobacteria phage MS2
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.5 Å/pix.
x 160 pix.
= 400. Å		2.5 Å/pix.
x 160 pix.
= 400. Å		2.5 Å/pix.
x 160 pix.
= 400. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.5 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.035 / Movie #1: 0.035
Minimum - Maximum-0.08399206 - 0.22530854
Average (Standard dev.)0.004143873 (±0.018184733)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions160160160
Spacing160160160
CellA=B=C: 400.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.52.52.5
M x/y/z160160160
origin x/y/z0.0000.0000.000
length x/y/z400.000400.000400.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS160160160
D min/max/mean-0.0840.2250.004

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Supplemental data

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Sample components

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Entire : Enterobacteria phage MS2

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

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Supramolecule #1: Enterobacteria phage MS2

SupramoleculeName: Enterobacteria phage MS2 / type: virus / ID: 1 / Parent: 0 / NCBI-ID: 329852 / Sci species name: Enterobacteria phage MS2 / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No

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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
GridDetails: unspecified
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TECNAI 20
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 34.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD

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Image processing

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 6.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 44987
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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