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

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Basic information

Entry
Database: EMDB / ID: 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
SampleFull phiX174 complexed with lipopolysaccharides before DNA ejection
  • Lipopolysaccharides (rough strains) from Salmonella enterica serotype typhimurium TV119 (Ra mutant)
SourceEnterobacteria phage phiX174 isolate Sanger (virus) / Salmonella enterica (bacteria)
Methodsingle particle reconstruction / cryo EM / 9.9 Å resolution
AuthorsRossmann MG / Sun Y / Klose T / Roznowski A / Fane BA / Pollack L / Tokuda J / Mauney A
Citation
Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Structural changes of tailless bacteriophage ΦX174 during penetration of bacterial cell walls.
Authors: Yingyuan Sun / Aaron P Roznowski / Joshua M Tokuda / Thomas Klose / Alexander Mauney / Lois Pollack / Bentley A Fane / Michael G Rossmann
#1: Journal: 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
DateDeposition: Sep 18, 2017 / Header (metadata) release: Oct 11, 2017 / Map release: Dec 6, 2017 / Last update: Jan 10, 2018

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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

Downloads & links

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Map

Fileemd_7033.map.gz (map file in CCP4 format, 16385 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
160 pix
3.24 Å/pix.
= 518.4 Å
160 pix
3.24 Å/pix.
= 518.4 Å
160 pix
3.24 Å/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
Contour Level:0.0287 (by author), 0.0287 (movie #1):
Minimum - Maximum-0.03602824 - 0.06672298
Average (Standard dev.)0.0011023843 (0.009172828)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions160160160
Origin000
Limit159159159
Spacing160160160
CellA=B=C: 518.4 Å
α=β=γ: 90 deg.

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
start NX/NY/NZ
NX/NY/NZ
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 ( map file in CCP4 format, 16385 KB )
Projections & Slices
AxesZYX
Projections
Slices (1/2)
Density Histograms
Data typeImage stored as Reals
Annotation detailsMask used in the first round of 3D classification
Space group number1

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Mask #2

Fileemd_7033_msk_2.map ( map file in CCP4 format, 16385 KB )
Projections & Slices
AxesZYX
Projections
Slices (1/2)
Density Histograms
Data typeImage stored as Reals
Annotation detailsMask used in the second round of 3D classification
Space group number1

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Mask #2~

Fileemd_7033_msk_2.map
Projections & Slices
AxesZYX
Projections
Slices (1/2)
Density Histograms

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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
Number of components: 2
MassTheoretical: 10 kDa

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Component #1: protein, Full phiX174 complexed with lipopolysaccharides before D...

ProteinName: Full phiX174 complexed with lipopolysaccharides before DNA ejection
Recombinant expression: No
MassTheoretical: 10 kDa
SourceSpecies: Enterobacteria phage phiX174 isolate Sanger (virus)

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Component #2: cellular-component, Lipopolysaccharides (rough strains) from Salm...

Cellular-componentName: Lipopolysaccharides (rough strains) from Salmonella enterica serotype typhimurium TV119 (Ra mutant)
Recombinant expression: No
SourceSpecies: Salmonella enterica (bacteria) / Strain: typhimurium TV119
Source (natural)Location in cell: outer membrane

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionSpecimen conc.: 1 mg/ml / pH: 7.4
VitrificationInstrument: GATAN CRYOPLUNGE 3 / Cryogen name: ETHANE / Temperature: 298 K / Humidity: 80 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 30 e/Å2 / Illumination mode: FLOOD BEAM
LensCs: 2.7 mm / Imaging mode: BRIGHT FIELD
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: GATAN K2 (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 2400
3D reconstructionAlgorithm: BACK PROJECTION / Software: RELION / Resolution: 9.9 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot
(resolution estimation)

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