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- EMDB-7033: Emptied phiX174 complexed with lipopolysaccharides after DNA ejection -

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Basic information

Entry
Database: EMDB / ID: EMD-7033
TitleEmptied phiX174 complexed with lipopolysaccharides after DNA ejection
Map dataEmptied phiX174 complexed with lipopolysaccharides after DNA ejection, low pass-filtered to 8 Angstrom resolution
Sample
  • Complex: Full phiX174 complexed with lipopolysaccharides before DNA ejection
    • Organelle or cellular component: Lipopolysaccharides (rough strains) from Salmonella enterica serotype typhimurium TV119 (Ra mutant)
Biological speciesEnterobacteria phage phiX174 isolate Sanger (virus) / Salmonella enterica (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 9.9 Å
AuthorsRossmann MG / Sun Y / Klose T / Roznowski A / Fane BA / Pollack L / Tokuda J / Mauney A
CitationJournal: Nature / Year: 2014
Title: Icosahedral bacteriophage ΦX174 forms a tail for DNA transport during infection.
Authors: Lei Sun / Lindsey N Young / Xinzheng Zhang / Sergei P Boudko / Andrei Fokine / Erica Zbornik / Aaron P Roznowski / Ian J Molineux / Michael G Rossmann / Bentley A Fane /
Abstract: Prokaryotic viruses have evolved various mechanisms to transport their genomes across bacterial cell walls. Many bacteriophages use a tail to perform this function, whereas tail-less phages rely on ...Prokaryotic viruses have evolved various mechanisms to transport their genomes across bacterial cell walls. Many bacteriophages use a tail to perform this function, whereas tail-less phages rely on host organelles. However, the tail-less, icosahedral, single-stranded DNA ΦX174-like coliphages do not fall into these well-defined infection processes. For these phages, DNA delivery requires a DNA pilot protein. Here we show that the ΦX174 pilot protein H oligomerizes to form a tube whose function is most probably to deliver the DNA genome across the host's periplasmic space to the cytoplasm. The 2.4 Å resolution crystal structure of the in vitro assembled H protein's central domain consists of a 170 Å-long α-helical barrel. The tube is constructed of ten α-helices with their amino termini arrayed in a right-handed super-helical coiled-coil and their carboxy termini arrayed in a left-handed super-helical coiled-coil. Genetic and biochemical studies demonstrate that the tube is essential for infectivity but does not affect in vivo virus assembly. Cryo-electron tomograms show that tubes span the periplasmic space and are present while the genome is being delivered into the host cell's cytoplasm. Both ends of the H protein contain transmembrane domains, which anchor the assembled tubes into the inner and outer cell membranes. The central channel of the H-protein tube is lined with amide and guanidinium side chains. This may be a general property of viral DNA conduits and is likely to be critical for efficient genome translocation into the host.
History
DepositionSep 18, 2017-
Header (metadata) releaseOct 11, 2017-
Map releaseDec 6, 2017-
UpdateJan 10, 2018-
Current statusJan 10, 2018Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0287
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.0287
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_7033.png

Downloads & links

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Map

FileDownload / File: emd_7033.map.gz / Format: CCP4 / Size: 15.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationEmptied phiX174 complexed with lipopolysaccharides after DNA ejection, low pass-filtered to 8 Angstrom resolution
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
3.24 Å/pix.
x 160 pix.
= 518.4 Å		3.24 Å/pix.
x 160 pix.
= 518.4 Å		3.24 Å/pix.
x 160 pix.
= 518.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 3.24 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0287 / Movie #1: 0.0287
Minimum - Maximum-0.03602824 - 0.06672298
Average (Standard dev.)0.0011023843 (±0.009172828)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions160160160
Spacing160160160
CellA=B=C: 518.4 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z3.243.243.24
M x/y/z160160160
origin x/y/z0.0000.0000.000
length x/y/z518.400518.400518.400
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS160160160
D min/max/mean-0.0360.0670.001

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Supplemental data

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Mask #1

Fileemd_7033_msk_1.map
Projections & Slices
AxesZYX

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Histogram

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Mask #2

Fileemd_7033_msk_2.map
Projections & Slices
AxesZYX

Projections

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Histogram

Histogram (log scale)

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Half map: Emptied phiX174 complexed with lipopolysaccharides after DNA ejection,...

Fileemd_7033_half_map_1.map
AnnotationEmptied phiX174 complexed with lipopolysaccharides after DNA ejection, half map #1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Emptied phiX174 complexed with lipopolysaccharides after DNA ejection,...

Fileemd_7033_half_map_2.map
AnnotationEmptied phiX174 complexed with lipopolysaccharides after DNA ejection, half map #2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Full phiX174 complexed with lipopolysaccharides before DNA ejection

EntireName: Full phiX174 complexed with lipopolysaccharides before DNA ejection
Components
  • Complex: Full phiX174 complexed with lipopolysaccharides before DNA ejection
    • Organelle or cellular component: Lipopolysaccharides (rough strains) from Salmonella enterica serotype typhimurium TV119 (Ra mutant)

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Supramolecule #1: Full phiX174 complexed with lipopolysaccharides before DNA ejection

SupramoleculeName: Full phiX174 complexed with lipopolysaccharides before DNA ejection
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Enterobacteria phage phiX174 isolate Sanger (virus)
Molecular weightTheoretical: 10 KDa

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Supramolecule #2: Lipopolysaccharides (rough strains) from Salmonella enterica sero...

SupramoleculeName: Lipopolysaccharides (rough strains) from Salmonella enterica serotype typhimurium TV119 (Ra mutant)
type: organelle_or_cellular_component / ID: 2 / Parent: 1
Source (natural)Organism: Salmonella enterica (bacteria) / Strain: typhimurium TV119 / Location in cell: outer membrane

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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

Concentration1 mg/mL
BufferpH: 7.4
VitrificationCryogen name: ETHANE / Chamber humidity: 80 % / Chamber temperature: 298 K / Instrument: GATAN CRYOPLUNGE 3
DetailsMixed with LPS and incubated at 33 degrees C for 1 minute

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 30.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 7500
CTF correctionSoftware - Name: CTFFIND3
Startup modelType of model: OTHER / Details: An icosahedral reconstruction from a small dataset
Final reconstructionNumber classes used: 1 / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 9.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 1.4) / Number images used: 2400
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: RELION
Final angle assignmentType: PROJECTION MATCHING
Final 3D classificationNumber classes: 4
FSC plot (resolution estimation)

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