+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-4150 | |||||||||
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Title | Structure of the baseplate of Siphophage J-1 | |||||||||
Map data | This is the baseplate of siphophage J-1 (Lactobacillus casei BL23 phage) with a part of the tail | |||||||||
Sample |
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Biological species | Lactobacillus phage J-1 (virus) | |||||||||
Method | single particle reconstruction / negative staining / Resolution: 20.0 Å | |||||||||
Authors | Cambillau C / Spinelli S / Dieterle ME / Piuri M | |||||||||
Citation | Journal: Mol Microbiol / Year: 2017 Title: Evolved distal tail carbohydrate binding modules of Lactobacillus phage J-1: a novel type of anti-receptor widespread among lactic acid bacteria phages. Authors: Maria-Eugenia Dieterle / Silvia Spinelli / Irina Sadovskaya / Mariana Piuri / Christian Cambillau / Abstract: Bacteriophage replication requires specific host-recognition. Some siphophages harbour a large complex, the baseplate, at the tip of their non-contractile tail. This baseplate holds receptor binding ...Bacteriophage replication requires specific host-recognition. Some siphophages harbour a large complex, the baseplate, at the tip of their non-contractile tail. This baseplate holds receptor binding proteins (RBPs) that can recognize the host cell-wall polysaccharide (CWPS) and specifically attach the phage to its host. While most phages possess a dedicated RBP, the phage J-1 that infects Lactobacillus casei seemed to lack one. It has been shown that the phage J-1 distal tail protein (Dit) plays a role in host recognition and that its sequence comprises two inserted modules compared with 'classical' Dits. The first insertion is similar to carbohydrate-binding modules (CBMs), whereas the second insertion remains undocumented. Here, we determined the structure of the second insertion and found it also similar to several CBMs. Expressed insertion CBM2, but not CBM1, binds to L. casei cells and neutralize phage attachment to the bacterial cell wall and the isolated and purified CWPS of L. casei BL23 prevents CBM2 attachment to the host. Electron microscopy single particle reconstruction of the J-1 virion baseplate revealed that CBM2 is projected at the periphery of Dit to optimally bind the CWPS receptor. Taken together, these results identify J-1 evolved Dit as the phage RBP. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_4150.map.gz | 157.7 KB | EMDB map data format | |
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Header (meta data) | emd-4150-v30.xml emd-4150.xml | 9 KB 9 KB | Display Display | EMDB header |
Images | emd_4150.png | 37.3 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-4150 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-4150 | HTTPS FTP |
-Validation report
Summary document | emd_4150_validation.pdf.gz | 236.2 KB | Display | EMDB validaton report |
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Full document | emd_4150_full_validation.pdf.gz | 235.4 KB | Display | |
Data in XML | emd_4150_validation.xml.gz | 4.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4150 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4150 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_4150.map.gz / Format: CCP4 / Size: 214.8 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | This is the baseplate of siphophage J-1 (Lactobacillus casei BL23 phage) with a part of the tail | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 4.83 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : virion's baseplate
Entire | Name: virion's baseplate |
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Components |
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-Supramolecule #1: virion's baseplate
Supramolecule | Name: virion's baseplate / type: complex / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Lactobacillus phage J-1 (virus) |
-Experimental details
-Structure determination
Method | negative staining |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7 |
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Staining | Type: NEGATIVE / Material: 1% uranyl acetate Details: stained with 10 microL of 1% uranyl acetate for 30 sec |
Details | The baseplate was boxed at the virion's tip |
-Electron microscopy
Microscope | FEI TECNAI SPIRIT |
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Image recording | Film or detector model: FEI EAGLE (2k x 2k) / Average electron dose: 2.0 e/Å2 |
Electron beam | Acceleration voltage: 120 kV / Electron source: LAB6 |
Electron optics | Illumination mode: OTHER / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Tecnai Spirit / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: OTHER |
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