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- EMDB-2335: The capsid of mycobacteriophage Araucaria -

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Basic information

Entry
Database: EMDB / ID: EMD-2335
TitleThe capsid of mycobacteriophage Araucaria
Map dataIcosahedral Reconstruction of the Araucaria capsid
Sample
  • Sample: Mycobacteriophage Araucaria Capsid
  • Virus: Mycobacteriophage Araucaria
Keywordsmycobacteriophage / Araucaria / single-particle / Mycobacterium abscessus subsp. bolletii / Siphoviridae / electron microscopy / mycobacteria.
Biological speciesMycobacteriophage Araucaria
Methodsingle particle reconstruction / negative staining / Resolution: 30.0 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 radius
  • Surface level: 0.03
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

EMD-2335.tif

Downloads & links

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Map

FileDownload / File: emd_2335.map.gz / Format: CCP4 / Size: 29.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationIcosahedral Reconstruction of the Araucaria capsid
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
4.95 Å/pix.
x 200 pix.
= 990. Å		4.95 Å/pix.
x 200 pix.
= 990. Å		4.95 Å/pix.
x 200 pix.
= 990. 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 - Maximum0.0 - 0.14693557
Average (Standard dev.)0.00272688 (±0.01485588)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 989.99994 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z4.954.954.95
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z990.000990.000990.000
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/NS200200200
D min/max/mean-0.0000.1470.003

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Supplemental data

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Sample components

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Entire : Mycobacteriophage Araucaria Capsid

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

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Supramolecule #1000: Mycobacteriophage Araucaria Capsid

SupramoleculeName: Mycobacteriophage Araucaria Capsid / type: sample / ID: 1000
Details: Capsid particles were selected from a sample containing whole phages.
Oligomeric state: Icosahedral / Number unique components: 1
Molecular weightExperimental: 2.8 MDa / Theoretical: 2.8 MDa / Method: Approximation with Chimera

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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 imposing ICOSAHEDRAL symmetry.
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 30.0 Å / Resolution method: OTHER / Software - Name: EMAN2, Spider, Xmipp / Number images used: 7431
Final angle assignmentDetails: ICOSAHEDRAL

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Atomic model buiding 1

Initial modelPDB ID:

1ohg

SoftwareName: Chimera
Details60 copies of the HK97 MCP hexamer were manually fitted and automatically refined.
RefinementSpace: REAL / Protocol: RIGID BODY FIT

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