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- EMDB-10929: 3D structure of bacteriophage phAPEC6 tail -

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Basic information

Entry
Database: EMDB / ID: EMD-10929
Title3D structure of bacteriophage phAPEC6 tail
Map dataEntire phAPEC6 tail. Resolution 25 A
Sample
  • Virus: Escherichia coli (E. coli)
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 25.0 Å
AuthorsWagemans J / Tsonos J / Holtappels D / Fortuna K / Hernalsteens JP / De Greve H / Estrozi LF / Bacia-Verloop M / Moriscot C / Noben JP ...Wagemans J / Tsonos J / Holtappels D / Fortuna K / Hernalsteens JP / De Greve H / Estrozi LF / Bacia-Verloop M / Moriscot C / Noben JP / Schoehn G / Lavigne R
CitationJournal: Int J Mol Sci / Year: 2020
Title: Structural Analysis of Jumbo Coliphage phAPEC6.
Authors: Jeroen Wagemans / Jessica Tsonos / Dominique Holtappels / Kiandro Fortuna / Jean-Pierre Hernalsteens / Henri De Greve / Leandro F Estrozi / Maria Bacia-Verloop / Christine Moriscot / Jean- ...Authors: Jeroen Wagemans / Jessica Tsonos / Dominique Holtappels / Kiandro Fortuna / Jean-Pierre Hernalsteens / Henri De Greve / Leandro F Estrozi / Maria Bacia-Verloop / Christine Moriscot / Jean-Paul Noben / Guy Schoehn / Rob Lavigne /
Abstract: The phAPEC6 genome encodes 551 predicted gene products, with the vast majority (83%) of unknown function. Of these, 62 have been identified as virion-associated proteins by mass spectrometry (ESI- ...The phAPEC6 genome encodes 551 predicted gene products, with the vast majority (83%) of unknown function. Of these, 62 have been identified as virion-associated proteins by mass spectrometry (ESI-MS/MS), including the major capsid protein (Gp225; present in 1620 copies), which shows a HK97 capsid protein-based fold. Cryo-electron microscopy experiments showed that the 350-kbp DNA molecule of virus phAPEC6 is packaged in at least 15 concentric layers in the phage capsid. A capsid inner body rod is also present, measuring about 91 nm by 18 nm and oriented along the portal axis. In the phAPEC6 contractile tail, 25 hexameric stacked rings can be distinguished, built of the identified tail sheath protein (Gp277). Cryo-EM reconstruction reveals the base of the unique hairy fibers observed during an initial transmission electron microscopy (TEM) analysis. These very unusual filaments are ordered at three annular positions along the contractile sheath, as well as around the capsid, and may be involved in host interaction.
History
DepositionApr 26, 2020-
Header (metadata) releaseMay 13, 2020-
Map releaseMay 13, 2020-
UpdateMay 13, 2020-
Current statusMay 13, 2020Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.156
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.156
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10929.png

Downloads & links

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Map

FileDownload / File: emd_10929.map.gz / Format: CCP4 / Size: 292.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationEntire phAPEC6 tail. Resolution 25 A
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
4.52 Å/pix.
x 425 pix.
= 1921. Å		4.52 Å/pix.
x 425 pix.
= 1921. Å		4.52 Å/pix.
x 425 pix.
= 1921. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 4.52 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.156 / Movie #1: 0.156
Minimum - Maximum-0.5276099 - 0.5811825
Average (Standard dev.)0.0007468529 (±0.034690678)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions425425425
Spacing425425425
CellA=B=C: 1921.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z4.524.524.52
M x/y/z425425425
origin x/y/z0.0000.0000.000
length x/y/z1921.0001921.0001921.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS425425425
D min/max/mean-0.5280.5810.001

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Supplemental data

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Sample components

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Entire : Escherichia coli

EntireName: Escherichia coli (E. coli)
Components
  • Virus: Escherichia coli (E. coli)

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Supramolecule #1: Escherichia coli

SupramoleculeName: Escherichia coli / type: virus / ID: 1 / Parent: 0 / NCBI-ID: 562 / Sci species name: Escherichia coli / Virus type: VIRION / Virus isolate: OTHER / Virus enveloped: No / Virus empty: No
Host (natural)Organism: 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

Concentration1 mg/mL
BufferpH: 7.5
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV / Details: Force 1, 2s blotting time.

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Electron microscopy

MicroscopeFEI POLARA 300
Image recordingFilm or detector model: KODAK SO-163 FILM / Number grids imaged: 1 / Number real images: 100 / Average electron dose: 20.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal magnification: 31000
Sample stageSpecimen holder model: OTHER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1024
Final reconstructionApplied symmetry - Point group: C6 (6 fold cyclic) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 25.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: SPIDER / Number images used: 500
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: SPIDER
Final angle assignmentType: PROJECTION MATCHING / Software - Name: SPIDER
Final 3D classificationSoftware - Name: SPIDER

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