[English] 日本語
Yorodumi
- EMDB-2336: The connector of mycobacteriophage Araucaria -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-2336
TitleThe connector of mycobacteriophage Araucaria
Map dataReconstruction of the Araucaria connector
Sample
  • Sample: Mycobacteriophage Araucaria Connector
  • Virus: Mycobacteriophage Araucaria
Keywordsmycobacteriophage / Araucaria / single-particle / Mycobacterium abscessus subsp. bolletii / Siphoviridae / electron microscopy / mycobacteria.
Biological speciesMycobacteriophage Araucaria
Methodsingle particle reconstruction / negative staining / Resolution: 28.0 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

-
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

Downloads & links

-
Map

FileDownload / File: emd_2336.map.gz / Format: CCP4 / Size: 3.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of the Araucaria connector
Voxel sizeX=Y=Z: 4.95 Å
Density
Contour LevelBy AUTHOR: 0.03 / Movie #1: 0.03
Minimum - Maximum-0.08707549 - 0.14360745
Average (Standard dev.)0.0037119 (±0.01629102)
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-0.0870.1440.004

-
Supplemental data

-
Sample components

-
Entire : Mycobacteriophage Araucaria Connector

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

-
Supramolecule #1000: Mycobacteriophage Araucaria Connector

SupramoleculeName: Mycobacteriophage Araucaria Connector / type: sample / ID: 1000
Details: Connector particles were selected from a sample containing whole phages.
Oligomeric state: C12 / Number unique components: 1
Molecular weightExperimental: 500 KDa / Method: Approximation with Chimera

-
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: Mycobacterium abscesus subsp. bolletii CIP108541T / synonym: BACTERIA(EUBACTERIA)
Virus shellShell ID: 1 / Name: Capsid T7 / Diameter: 600 Å / T number (triangulation number): 7

-
Experimental details

-
Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

-
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

-
Electron microscopy

MicroscopeFEI TECNAI 12
Electron beamAcceleration voltage: 120 kV / Electron source: LAB6
Electron opticsCalibrated magnification: 48500 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / 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
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

-
Image processing

Final angle assignmentDetails: C12
Final reconstructionApplied symmetry - Point group: C12 (12 fold cyclic) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 28.0 Å / Resolution method: OTHER / Software - Name: EMAN2, Spider, Xmipp / Number images used: 6740
DetailsParticles were processed using a Maximum Likelihood approach.

-
Atomic model buiding 1

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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242):Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more