|Entry||Database: EMDB / ID: EMD-2817|
|Title||Electron cryoEM structure of lactococcal siphophage 1358 virion|
|Sample||Baseplate of phage 1358:|
|Keywords||Lactococcus lactis / Siphoviridae / electron microscopy / 1358 phage / baseplate|
|Biological species||Lactococcus phage 1358 (bacteriophage)|
|Method||single particle reconstruction / cryo EM / Resolution: 24 Å|
|Authors||Spinelli S / Bebeacua C / Orlov I / Tremblay D / Klaholz B / Moineau S / Cambillau C|
|Citation||Journal: J Virol / Year: 2014|
Title: Cryo-electron microscopy structure of lactococcal siphophage 1358 virion.
Authors: Silvia Spinelli / Cecilia Bebeacua / Igor Orlov / Denise Tremblay / Bruno P Klaholz / Sylvain Moineau / Christian Cambillau /
Abstract: Lactococcus lactis, a Gram(+) lactic acid-producing bacterium used for the manufacture of several fermented dairy products, is subject to infection by diverse virulent tailed phages, leading to ...Lactococcus lactis, a Gram(+) lactic acid-producing bacterium used for the manufacture of several fermented dairy products, is subject to infection by diverse virulent tailed phages, leading to industrial fermentation failures. This constant viral risk has led to a sustained interest in the study of their biology, diversity, and evolution. Lactococcal phages now constitute a wide ensemble of at least 10 distinct genotypes within the Caudovirales order, many of them belonging to the Siphoviridae family. Lactococcal siphophage 1358, currently the only member of its group, displays a noticeably high genomic similarity to some Listeria phages as well as a host range limited to a few L. lactis strains. These genomic and functional characteristics stimulated our interest in this phage. Here, we report the cryo-electron microscopy structure of the complete 1358 virion. Phage 1358 exhibits noteworthy features, such as a capsid with dextro handedness and protruding decorations on its capsid and tail. Observations of the baseplate of virion particles revealed at least two conformations, a closed and an open, activated form. Functional assays uncovered that the adsorption of phage 1358 to its host is Ca(2+) independent, but this cation is necessary to complete its lytic cycle. Taken together, our results provide the complete structural picture of a unique lactococcal phage and expand our knowledge on the complex baseplate of phages of the Siphoviridae family.
Importance: Phages of Lactococcus lactis are investigated mainly because they are sources of milk fermentation failures in the dairy industry. Despite the availability of several antiphage measures, ...Importance: Phages of Lactococcus lactis are investigated mainly because they are sources of milk fermentation failures in the dairy industry. Despite the availability of several antiphage measures, new phages keep emerging in this ecosystem. In this study, we provide the cryo-electron microscopy reconstruction of a unique lactococcal phage that possesses genomic similarity to particular Listeria phages and has a host range restricted to only a minority of L. lactis strains. The capsid of phage 1358 displays the almost unique characteristic of being dextro handed. Its capsid and tail exhibit decorations that we assigned to nonspecific sugar binding modules. We observed the baseplate of 1358 in two conformations, a closed and an open form. We also found that the adsorption to its host, but not infection, is Ca(2+) independent. Overall, this study advances our understanding of the adhesion mechanisms of siphophages.
|Structure viewer||EM map: |
Downloads & links
|File||Download / File: emd_2817.map.gz / Format: CCP4 / Size: 100.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)|
|Projections & slices|
Images are generated by Spider.
|Voxel size||X=Y=Z: 1.92 Å|
|Symmetry||Space group: 1|
CCP4 map header:
-Entire Baseplate of phage 1358
|Entire||Name: Baseplate of phage 1358 / Details: The sample contains the whole phage. / Number of components: 1 / Oligomeric State: Hexamer|
-Component #1: virus, Lactococcus phage 1358
|Virus||Name: Lactococcus phage 1358 / Class: OTHER / Empty: No / Enveloped: No / Isolate: SPECIES|
|Species||Species: Lactococcus phage 1358 (bacteriophage)|
|Source (natural)||Host Species: Lactoccocus lactis / Host category: BACTERIA(EUBACTERIA)|
|Shell #1||Name of element: T7 / Diameter: 600 Å / T number (triangulation number): 7|
|Specimen||Specimen state: Particle / Method: cryo EM|
|Sample solution||Buffer solution: Phage Buffer / pH: 7.4|
|Vitrification||Instrument: FEI VITROBOT MARK I / Cryogen name: ETHANE / Humidity: 95 % / Method: Blot for 3 seconds before plunging. / Details: cryo plunge-freezing|
-Electron microscopy imaging
Model: Tecnai F30 / Image courtesy: FEI Company
|Imaging||Microscope: FEI TECNAI F30 / Date: Sep 1, 2012|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 10 e/Å2 / Illumination mode: SPOT SCAN|
|Lens||Magnification: 59000 X (nominal)|
Astigmatism: Objective lens astigmatism was corrected at 100,000 times magnification.
Cs: 2.2 mm / Imaging mode: BRIGHT FIELD / Defocus: 1000 - 3500 nm / Energy filter: FEI
|Specimen Holder||Model: GATAN LIQUID NITROGEN|
|Camera||Detector: FEI EAGLE (4k x 4k)|
|Image acquisition||Number of digital images: 200 / Sampling size: 16 µm / Bit depth: 16|
|Processing||Method: single particle reconstruction / Applied symmetry: C6 (6回回転対称) / Number of projections: 2415 |
Details: Baseplate reconstructed using a Maximum Likelihood Approach.
|3D reconstruction||Algorithm: Maximum Likelihood / Euler angles: C6 / Software: EMAN2, SPIDER, Xmipp / CTF correction: Images / Resolution: 24 Å / Resolution method: FSC and 1/2-bit cut-off|
-Aug 12, 2020. New: Covid-19 info
New: Covid-19 info
Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data
-Mar 5, 2020. Novel coronavirus structure data
Novel coronavirus structure data
- International Committee on Taxonomy of Viruses (ICTV) defined the short name of the 2019 coronavirus as "SARS-CoV-2".
The species Severe acute respiratory syndrome-related coronavirus: classifying 2019-nCoV and naming it SARS-CoV-2 - nature microbiology
- In the structure databanks used in Yorodumi, some data are registered as the other names, "COVID-19 virus" and "2019-nCoV". Here are the details of the virus and the list of structure data.
Related info.:Yorodumi Speices / Aug 12, 2020. New: Covid-19 info
+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. (see PDBe EMDB page)
- The EM Navigator/Yorodumi systems omit the EMD- prefix.
Related info.:Q: What is "EMD"? / ID/Accession-code notation in Yorodumi/EM Navigator
+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. See below links for details.
- 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.
+Jun 16, 2017. Omokage search with filter
Omokage search with filter
- Result of Omokage search can be filtered by keywords and the database types
Related info.:Omokage search
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.
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