+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-1792 | |||||||||
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Title | EM map of TP901-1 BppU-BppL complex | |||||||||
Map data | EM map of TP9101-1 BppU-BppL complex | |||||||||
Sample |
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Keywords | Bacteriophage / TP9101-1 / BppU / BppL / ORF 48 / ORF 49 | |||||||||
Biological species | Lactococcus phage TP901-1 (virus) | |||||||||
Method | single particle reconstruction / negative staining / Resolution: 24.8 Å | |||||||||
Authors | Bron P | |||||||||
Citation | Journal: J Biol Chem / Year: 2010 Title: Structure and molecular assignment of lactococcal phage TP901-1 baseplate. Authors: Cecilia Bebeacua / Patrick Bron / Livia Lai / Christina Skovgaard Vegge / Lone Brøndsted / Silvia Spinelli / Valérie Campanacci / David Veesler / Marin van Heel / Christian Cambillau / Abstract: P335 lactococcal phages infect the gram(+) bacterium Lactococcus lactis using a large multiprotein complex located at the distal part of the tail and termed baseplate (BP). The BP harbors the ...P335 lactococcal phages infect the gram(+) bacterium Lactococcus lactis using a large multiprotein complex located at the distal part of the tail and termed baseplate (BP). The BP harbors the receptor-binding proteins (RBPs), which allow the specific recognition of saccharidic receptors localized on the host cell surface. We report here the electron microscopic structure of the phage TP901-1 wild-type BP as well as those of two mutants bppL (-) and bppU(-), lacking BppL (the RBPs) or both peripheral BP components (BppL and BppU), respectively. We also achieved an electron microscopic reconstruction of a partial BP complex, formed by BppU and BppL. This complex exhibits a tripod shape and is composed of nine BppLs and three BppUs. These structures, combined with light-scattering measurements, led us to propose that the TP901-1 BP harbors six tripods at its periphery, located around the central tube formed by ORF46 (Dit) hexamers, at its proximal end, and a ORF47 (Tal) trimer at its distal extremity. A total of 54 BppLs (18 RBPs) are thus available to mediate host anchoring with a large apparent avidity. TP901-1 BP exhibits an infection-ready conformation and differs strikingly from the lactococcal phage p2 BP, bearing only 6 RBPs, and which needs a conformational change to reach its activated state. The comparison of several Siphoviridae structures uncovers a close organization of their central BP core whereas striking differences occur at the periphery, leading to diverse mechanisms of host recognition. | |||||||||
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_1792.map.gz | 2.6 MB | EMDB map data format | |
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Header (meta data) | emd-1792-v30.xml emd-1792.xml | 10.1 KB 10.1 KB | Display Display | EMDB header |
Images | EMD-1792.png | 46 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-1792 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-1792 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_1792.map.gz / Format: CCP4 / Size: 2.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | EM map of TP9101-1 BppU-BppL complex | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 4 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 : BppU/BppL complex from Lactococcal Phage TP901-1
Entire | Name: BppU/BppL complex from Lactococcal Phage TP901-1 |
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Components |
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-Supramolecule #1000: BppU/BppL complex from Lactococcal Phage TP901-1
Supramolecule | Name: BppU/BppL complex from Lactococcal Phage TP901-1 / type: sample / ID: 1000 Oligomeric state: one trimer of BppU and three trimers of BppL Number unique components: 2 |
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-Macromolecule #1: BppU
Macromolecule | Name: BppU / type: protein_or_peptide / ID: 1 / Name.synonym: ORF48 / Number of copies: 1 / Oligomeric state: Monomer / Recombinant expression: Yes |
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Source (natural) | Organism: Lactococcus phage TP901-1 (virus) |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
-Macromolecule #2: BppL
Macromolecule | Name: BppL / type: protein_or_peptide / ID: 2 / Name.synonym: ORF49 / Number of copies: 3 / Oligomeric state: Trimer / Recombinant expression: Yes |
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Source (natural) | Organism: Lactococcus phage TP901-1 (virus) |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
-Experimental details
-Structure determination
Method | negative staining |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.05 mg/mL |
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Buffer | pH: 7.5 / Details: 10 mM Hepes, 150 mM NaCl, 1 mM PMSF |
Staining | Type: NEGATIVE Details: Grids with adsorbed protein floated on 1% uranyl acetate for 1 min. |
Grid | Details: 400 mesh cupper griid |
Vitrification | Cryogen name: NONE / Instrument: OTHER |
-Electron microscopy
Microscope | JEOL 2200FS |
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Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 50000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.0 mm / Nominal defocus max: 1.0 µm / Nominal defocus min: 0.4 µm / Nominal magnification: 50000 |
Specialist optics | Energy filter - Name: Omega filter / Energy filter - Lower energy threshold: 0.0 eV / Energy filter - Upper energy threshold: 20.0 eV |
Sample stage | Specimen holder: Eucentric / Specimen holder model: JEOL |
Alignment procedure | Legacy - Astigmatism: Astigmatism was corrected at 150,000 times magnification |
Details | Low-dose imaging |
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: 8 / Average electron dose: 18 e/Å2 / Bits/pixel: 8 |
-Image processing
CTF correction | Details: Each particle |
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Final reconstruction | Applied symmetry - Point group: C3 (3 fold cyclic) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 24.8 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: IMAGIC V / Number images used: 8314 |
-Atomic model buiding 1
Initial model | PDB ID: |
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Details | The trimers were separately fitted by manual docking and refined using the docking program integrated into Chimera |
Refinement | Space: REAL / Protocol: RIGID BODY FIT |