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- EMDB-0448: F-pilus/MS2 complex (Class 2 map with genome masked out) -

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Basic information

Entry
Database: EMDB / ID: EMD-0448
TitleF-pilus/MS2 complex (Class 2 map with genome masked out)
Map dataEscherichia coli F-pilus and Enterobacteria phage MS2 complex (Class 2 map with phage genome masked out).
Sample
  • Complex: F-pilus/MS2 complex
    • Complex: Enterobacteria phage MS2
    • Complex: F-plius
Biological speciesEnterobacteria phage MS2 (virus) / Escherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.6 Å
AuthorsMeng R / Jiang M / Zhang J
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research InstituteP41GM103832 United States
National Institutes of Health/National Human Genome Research InstituteP01AI095208 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
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: 0.03
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0448.png

Downloads & links

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Map

FileDownload / File: emd_0448.map.gz / Format: CCP4 / Size: 38.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationEscherichia coli F-pilus and Enterobacteria phage MS2 complex (Class 2 map with phage genome masked out).
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.46 Å/pix.
x 216 pix.
= 531.36 Å		2.46 Å/pix.
x 216 pix.
= 531.36 Å		2.46 Å/pix.
x 216 pix.
= 531.36 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.46 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.03 / Movie #1: 0.03
Minimum - Maximum-0.10436843 - 0.21224126
Average (Standard dev.)0.0015741542 (±0.011224586)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions216216216
Spacing216216216
CellA=B=C: 531.36 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.462.462.46
M x/y/z216216216
origin x/y/z0.0000.0000.000
length x/y/z531.360531.360531.360
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS216216216
D min/max/mean-0.1040.2120.002

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Supplemental data

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Additional map: Escherichia coli F-pilus and Enterobacteria phage MS2 complex...

Fileemd_0448_additional.map
AnnotationEscherichia coli F-pilus and Enterobacteria phage MS2 complex (Class 2 map with phage genome), additional map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : F-pilus/MS2 complex

EntireName: F-pilus/MS2 complex
Components
  • Complex: F-pilus/MS2 complex
    • Complex: Enterobacteria phage MS2
    • Complex: F-plius

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Supramolecule #1: F-pilus/MS2 complex

SupramoleculeName: F-pilus/MS2 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2

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Supramolecule #2: Enterobacteria phage MS2

SupramoleculeName: Enterobacteria phage MS2 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Enterobacteria phage MS2 (virus)

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Supramolecule #3: F-plius

SupramoleculeName: F-plius / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Escherichia coli (E. coli)

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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

MicroscopeJEOL 3200FSC
Specialist opticsEnergy filter - Slit width: 30 eV
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average exposure time: 8.0 sec. / Average electron dose: 37.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD

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Image processing

CTF correctionSoftware - Name: Gctf (ver. 1.06)
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 5.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.1) / Number images used: 58447
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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