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Yorodumi- EMDB-1706: Cryo-EM map of Lactococcal phage p2 baseplate consisting of ORF 1... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-1706 | |||||||||
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Title | Cryo-EM map of Lactococcal phage p2 baseplate consisting of ORF 15, 16 and 18. | |||||||||
Map data | Cryo-EM map of p2 phage baseplate | |||||||||
Sample |
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Keywords | Baseplate / phage / P2 / Siphoviridae / orf 15 / orf 16 / orf 18 / RBP / cryo-EM | |||||||||
Biological species | Lactococcus lactis phage p2 (virus) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 26.0 Å | |||||||||
Authors | Sciara G / Bebeacua C / Bron P / Tremblay D / Ortiz-Lombardia M / Lichiere J / Van Heel M / Campanacci V / Moineau S / Cambillau C | |||||||||
Citation | Journal: Proc Natl Acad Sci U S A / Year: 2010 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 |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_1706.map.gz | 625.4 KB | EMDB map data format | |
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Header (meta data) | emd-1706-v30.xml emd-1706.xml | 10.1 KB 10.1 KB | Display Display | EMDB header |
Images | 1706.png | 360.1 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-1706 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-1706 | HTTPS FTP |
-Validation report
Summary document | emd_1706_validation.pdf.gz | 195.9 KB | Display | EMDB validaton report |
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Full document | emd_1706_full_validation.pdf.gz | 195 KB | Display | |
Data in XML | emd_1706_validation.xml.gz | 5.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1706 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1706 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_1706.map.gz / Format: CCP4 / Size: 8.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Cryo-EM map of p2 phage baseplate | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 4.37 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 : Over-expressed Lactococcal phage p2 baseplate
Entire | Name: Over-expressed Lactococcal phage p2 baseplate |
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Components |
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-Supramolecule #1000: Over-expressed Lactococcal phage p2 baseplate
Supramolecule | Name: Over-expressed Lactococcal phage p2 baseplate / type: sample / ID: 1000 Oligomeric state: One homotrimer of ORF16 binds to two hexamers of ORF15 and binds to six homotrimers of ORF18 Number unique components: 1 |
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Molecular weight | Experimental: 1 MDa |
-Macromolecule #1: p2 Lactoccocal phage baseplate
Macromolecule | Name: p2 Lactoccocal phage baseplate / type: protein_or_peptide / ID: 1 / Name.synonym: p2 baseplate / Details: Complexes was cross-linked by glutaraldehyde / Recombinant expression: Yes |
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Source (natural) | Organism: Lactococcus lactis phage p2 (virus) |
Molecular weight | Experimental: 1 MDa |
Recombinant expression | Organism: Escherichia coli (E. coli) / Recombinant plasmid: Gateway pDEST14 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.07 mg/mL |
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Buffer | pH: 7.5 / Details: 10mM HEPES, 150mM NaCl, 0.02% Glutaraldehyde |
Grid | Details: R2.2 Quantifoil |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 92 % / Chamber temperature: 103.15 K / Instrument: GATAN CRYOPLUNGE 3 / Details: Vitrification instrument: CP3 Gatan / Method: Blot for 1 second before plunging |
-Electron microscopy
Microscope | JEOL 2200FS |
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Temperature | Average: 98.15 K |
Alignment procedure | Legacy - Astigmatism: Objective lens astigmatism was corrected at 200,000 times magnification |
Specialist optics | Energy filter - Name: Omega / Energy filter - Lower energy threshold: 0.0 eV / Energy filter - Upper energy threshold: 20.0 eV |
Image recording | Category: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: NIKON SUPER COOLSCAN 9000 / Digitization - Sampling interval: 10 µm / Number real images: 46 / Average electron dose: 18 e/Å2 / Bits/pixel: 8 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 45710 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 2.6 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 50000 |
Sample stage | Specimen holder: Eucentric / Specimen holder model: GATAN LIQUID NITROGEN |
-Image processing
CTF correction | Details: Each particle |
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Final reconstruction | Applied symmetry - Point group: C6 (6 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 26.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: IMAGIC V |
Final angle assignment | Details: beta 0 degrees, gamma 90 |
Final two d classification | Number classes: 263 |