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- EMDB-2338: The baseplate of mycobacteriophage Araucaria -

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Basic information

Entry
Database: EMDB / ID: EMD-2338
TitleThe baseplate of mycobacteriophage Araucaria
Map dataReconstruction of the Araucaria baseplate
Sample
  • Sample: Mycobacteriophage Araucaria Baseplate
  • Virus: Mycobacteriophage Araucaria
Keywordsmycobacteriophage / Araucaria / single-particle / Mycobacterium abscessus subsp. bolletii / Siphoviridae / electron microscopy / mycobacteria.
Biological speciesMycobacteriophage Araucaria
Methodsingle particle reconstruction / negative staining / Resolution: 26.0 Å
AuthorsSassi M / Bebeacua C / Drancourt M / Cambillau C
CitationJournal: J Virol / Year: 2013
Title: The first structure of a mycobacteriophage, the Mycobacterium abscessus subsp. bolletii phage Araucaria.
Authors: Mohamed Sassi / Cecilia Bebeacua / Michel Drancourt / Christian Cambillau /
Abstract: The unique characteristics of the waxy mycobacterial cell wall raise questions about specific structural features of their bacteriophages. No structure of any mycobacteriophage is available, although ...The unique characteristics of the waxy mycobacterial cell wall raise questions about specific structural features of their bacteriophages. No structure of any mycobacteriophage is available, although ∼3,500 have been described to date. To fill this gap, we embarked in a genomic and structural study of a bacteriophage from Mycobacterium abscessus subsp. bolletii, a member of the Mycobacterium abscessus group. This opportunistic pathogen is responsible for respiratory tract infections in patients with lung disorders, particularly cystic fibrosis. M. abscessus subsp. bolletii was isolated from respiratory tract specimens, and bacteriophages were observed in the cultures. We report here the genome annotation and characterization of the M. abscessus subsp. bolletii prophage Araucaria, as well as the first single-particle electron microscopy reconstruction of the whole virion. Araucaria belongs to Siphoviridae and possesses a 64-kb genome containing 89 open reading frames (ORFs), among which 27 could be annotated with certainty. Although its capsid and connector share close similarity with those of several phages from Gram-negative (Gram(-)) or Gram(+) bacteria, its most distinctive characteristic is the helical tail decorated by radial spikes, possibly host adhesion devices, according to which the phage name was chosen. Its host adsorption device, at the tail tip, assembles features observed in phages binding to protein receptors, such as phage SPP1. All together, these results suggest that Araucaria may infect its mycobacterial host using a mechanism involving adhesion to cell wall saccharides and protein, a feature that remains to be further explored.
History
DepositionMar 20, 2013-
Header (metadata) releaseApr 17, 2013-
Map releaseJul 24, 2013-
UpdateJul 24, 2013-
Current statusJul 24, 2013Processing site: PDBe / 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 cylindrical radius
  • Surface level: 0.03
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

EMD-2338.tif

Downloads & links

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Map

FileDownload / File: emd_2338.map.gz / Format: CCP4 / Size: 3.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of the Araucaria baseplate
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
4.95 Å/pix.
x 100 pix.
= 495. Å		4.95 Å/pix.
x 100 pix.
= 495. Å		4.95 Å/pix.
x 100 pix.
= 495. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 4.95 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.03 / Movie #1: 0.03
Minimum - Maximum-0.21920949 - 0.35790157
Average (Standard dev.)0.00307062 (±0.02232647)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions100100100
Spacing100100100
CellA=B=C: 494.99997 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z4.954.954.95
M x/y/z100100100
origin x/y/z0.0000.0000.000
length x/y/z495.000495.000495.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-27-15-36
NX/NY/NZ553173
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS100100100
D min/max/mean-0.2190.3580.003

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Supplemental data

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Sample components

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Entire : Mycobacteriophage Araucaria Baseplate

EntireName: Mycobacteriophage Araucaria Baseplate
Components
  • Sample: Mycobacteriophage Araucaria Baseplate
  • Virus: Mycobacteriophage Araucaria

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Supramolecule #1000: Mycobacteriophage Araucaria Baseplate

SupramoleculeName: Mycobacteriophage Araucaria Baseplate / type: sample / ID: 1000
Details: Baseplate particles were selected from a sample containing whole phages.
Oligomeric state: C6 / Number unique components: 1

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Supramolecule #1: Mycobacteriophage Araucaria

SupramoleculeName: Mycobacteriophage Araucaria / type: virus / ID: 1 / Name.synonym: Araucaria / Sci species name: Mycobacteriophage Araucaria / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No / Syn species name: Araucaria
Host (natural)Organism: Mycobacterium abscessus subsp. bolletii (bacteria)
Strain: CIP108541T / synonym: BACTERIA(EUBACTERIA)
Virus shellShell ID: 1 / Name: Capsid T7 / Diameter: 600 Å / T number (triangulation number): 7

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Experimental details

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Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7 / Details: PBS Buffer
StainingType: NEGATIVE
Details: Grids with adsorbed viral particles were stained with 2% uranyl acetate for 20 seconds.
GridDetails: 300 copper mesh grids with a film of colodion and carbon
VitrificationCryogen name: NONE / Instrument: OTHER

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Electron microscopy

MicroscopeFEI TECNAI 12
Alignment procedureLegacy - Astigmatism: Objective lens astigmatism was corrected at 150,000 times magnification
DateJul 1, 2012
Image recordingCategory: CCD / Film or detector model: GENERIC CCD (2k x 2k) / Number real images: 1500 / Average electron dose: 10 e/Å2
Electron beamAcceleration voltage: 120 kV / Electron source: LAB6
Electron opticsCalibrated magnification: 48500 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2 mm / Nominal defocus max: 1.5 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 48500
Sample stageSpecimen holder: Room temperature holder / Specimen holder model: SIDE ENTRY, EUCENTRIC

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Image processing

DetailsParticles were processed using a Maximum Likelihood approach.
Final reconstructionApplied symmetry - Point group: C6 (6 fold cyclic) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 26.0 Å / Resolution method: OTHER / Software - Name: EMAN2, Spider, Xmipp / Number images used: 6460
Final angle assignmentDetails: C6

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Atomic model buiding 1

Initial modelPDB ID:

2x8k

SoftwareName: Chimera
DetailsAtomic coordinates were manually fitted and automatically refined.
RefinementSpace: REAL / Protocol: RIGID BODY FIT

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