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- EMDB-1699: Structure of Lactococcal Phage p2 Baseplate and its Mechanism of ... -
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Basic information
Entry | Database: EMDB / ID: EMD-1699 | |||||||||
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Title | Structure of Lactococcal Phage p2 Baseplate and its Mechanism of Activation | |||||||||
![]() | This is the ccp4 file of the EM 3D reconstruction of the baseplate of the wild-type p2 bacteriophage. The map is associated to the following PDB entries: PDB: 2WZP: BP closed form PDB: 2X53: BP Activated form C2 PDB: 2X54 + 2X5A: BP Activated form P2 | |||||||||
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![]() | p2 / baseplate / phage / EM | |||||||||
Function / homology | ![]() symbiont genome ejection through host cell envelope, long flexible tail mechanism / virus tail, baseplate / virus tail / entry receptor-mediated virion attachment to host cell / cell adhesion / symbiont entry into host cell / virion attachment to host cell Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / negative staining / Resolution: 22.0 Å | |||||||||
![]() | Sciara G / Bebeacua C / Bron P / Tremblay D / Ortiz-Lombardia M / Lichiere J / van Heel M / Campanacci V / Moineau S / Cambillau C | |||||||||
![]() | ![]() Title: Structure of lactococcal phage p2 baseplate and its mechanism of activation. Authors: Giuliano Sciara / Cecilia Bebeacua / Patrick Bron / Denise Tremblay / Miguel Ortiz-Lombardia / Julie Lichière / Marin van Heel / Valérie Campanacci / Sylvain Moineau / Christian Cambillau / ![]() Abstract: Siphoviridae is the most abundant viral family on earth which infects bacteria as well as archaea. All known siphophages infecting gram+ Lactococcus lactis possess a baseplate at the tip of their ...Siphoviridae is the most abundant viral family on earth which infects bacteria as well as archaea. All known siphophages infecting gram+ Lactococcus lactis possess a baseplate at the tip of their tail involved in host recognition and attachment. Here, we report analysis of the p2 phage baseplate structure by X-ray crystallography and electron microscopy and propose a mechanism for the baseplate activation during attachment to the host cell. This approximately 1 MDa, Escherichia coli-expressed baseplate is composed of three protein species, including six trimers of the receptor-binding protein (RBP). RBPs host-recognition domains point upwards, towards the capsid, in agreement with the electron-microscopy map of the free virion. In the presence of Ca(2+), a cation mandatory for infection, the RBPs rotated 200 degrees downwards, presenting their binding sites to the host, and a channel opens at the bottom of the baseplate for DNA passage. These conformational changes reveal a novel siphophage activation and host-recognition mechanism leading ultimately to DNA ejection. | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 828.7 KB | ![]() | |
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Header (meta data) | ![]() ![]() | 9 KB 9 KB | Display Display | ![]() |
Images | ![]() | 80.9 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 195.7 KB | Display | ![]() |
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Full document | ![]() | 194.9 KB | Display | |
Data in XML | ![]() | 5.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6zjjM ![]() 1706C ![]() 2wzpC ![]() 2x53C ![]() 4v5iC C: citing same article ( M: atomic model generated by this map |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | This is the ccp4 file of the EM 3D reconstruction of the baseplate of the wild-type p2 bacteriophage. The map is associated to the following PDB entries: PDB: 2WZP: BP closed form PDB: 2X53: BP Activated form C2 PDB: 2X54 + 2X5A: BP Activated form P2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 4.64 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : P2 baseplate wild-type
Entire | Name: P2 baseplate wild-type |
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Components |
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-Supramolecule #1000: P2 baseplate wild-type
Supramolecule | Name: P2 baseplate wild-type / type: sample / ID: 1000 / Oligomeric state: Homohexamer / Number unique components: 1 |
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Molecular weight | Experimental: 1 MDa / Theoretical: 1 MDa |
-Macromolecule #1: P2 baseplate
Macromolecule | Name: P2 baseplate / type: protein_or_peptide / ID: 1 / Name.synonym: P2 baseplate / Number of copies: 6 / Oligomeric state: Hexamer / Recombinant expression: No |
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Source (natural) | Organism: ![]() |
-Experimental details
-Structure determination
Method | negative staining |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Staining | Type: NEGATIVE Details: Sample was incubated on glow-discharged grid for approximately one minute. 2% uranyl acetate was applied onto the sample and left for about 30 seconds. |
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Vitrification | Cryogen name: NONE / Instrument: OTHER |
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Electron microscopy
Microscope | FEI/PHILIPS CM200FEG/UT |
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Alignment procedure | Legacy - Astigmatism: corrected at 200,000 times magnification |
Image recording | Digitization - Sampling interval: 2.32 µm / Number real images: 1000 / Average electron dose: 10 e/Å2 |
Tilt angle min | 0 |
Tilt angle max | 0 |
Electron beam | Acceleration voltage: 200 kV / Electron source: ![]() |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2.2 mm / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 38000 |
Sample stage | Specimen holder: Room Temperature / Specimen holder model: OTHER |
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Image processing
CTF correction | Details: CCD Images |
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Final reconstruction | Applied symmetry - Point group: C6 (6 fold cyclic) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 22.0 Å / Resolution method: OTHER / Software - Name: IMAGIC-5 Details: Initial map calculated with class averages. Final map calculated after projection matching refinement. Number images used: 9486 |
Final angle assignment | Details: IMAGIC |