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- EMDB-0338: MS2 / F-pilus complex -

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Basic information

Entry
Database: EMDB / ID: EMD-0338
TitleMS2 / F-pilus complex
Map data
Sample
  • Complex: MS2 / F-pilus complex
Biological speciesEnterobacterio phage MS2 (virus)
Methodsubtomogram averaging / cryo EM / Resolution: 32.3 Å
AuthorsHu B
Funding support United States, 1 items
OrganizationGrant numberCountry
Welch FoundationAU-1953-20180324 United States
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
DepositionNov 17, 2018-
Header (metadata) releaseFeb 20, 2019-
Map releaseJul 31, 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: 7.6
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 7.6
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0338.png

Downloads & links

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Map

FileDownload / File: emd_0338.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
9 Å/pix.
x 240 pix.
= 2160. Å		9 Å/pix.
x 240 pix.
= 2160. Å		9 Å/pix.
x 240 pix.
= 2160. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 9 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 7.6 / Movie #1: 7.6
Minimum - Maximum-50.259932999999997 - 67.136809999999997
Average (Standard dev.)-0.00000000000035 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-120-120-120
Dimensions240240240
Spacing240240240
CellA=B=C: 2160.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z999
M x/y/z240240240
origin x/y/z0.0000.0000.000
length x/y/z2160.0002160.0002160.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-120-120-120
NC/NR/NS240240240
D min/max/mean-50.26067.137-0.000

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Supplemental data

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Sample components

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Entire : MS2 / F-pilus complex

EntireName: MS2 / F-pilus complex
Components
  • Complex: MS2 / F-pilus complex

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Supramolecule #1: MS2 / F-pilus complex

SupramoleculeName: MS2 / F-pilus complex / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Enterobacterio phage MS2 (virus)

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statecell

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Sample preparation

BufferpH: 7
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI POLARA 300
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 1.7 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 32.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number subtomograms used: 1245
ExtractionNumber tomograms: 30 / Number images used: 1245
Final angle assignmentType: OTHER

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