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Open data
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Basic information
Entry | ![]() | |||||||||||||||
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Title | PhiCPV4 bacteriophage Portal Protein | |||||||||||||||
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![]() | Bacteriophage / portal protein / cryoEM / VIRAL PROTEIN | |||||||||||||||
Function / homology | Portal protein Gp10 / Phage Connector (GP10) / Portal protein Gp10 superfamily / Connector protein![]() | |||||||||||||||
Biological species | ![]() ![]() ![]() | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.8 Å | |||||||||||||||
![]() | Javed A / Villanueva H | |||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Cryo-EM Structures of Two Bacteriophage Portal Proteins Provide Insights for Antimicrobial Phage Engineering. Authors: Abid Javed / Hugo Villanueva / Shadikejiang Shataer / Sara Vasciaveo / Renos Savva / Elena V Orlova / ![]() Abstract: Widespread antibiotic resistance has returned attention to bacteriophages as a means of managing bacterial pathogenesis. Synthetic biology approaches to engineer phages have demonstrated genomic ...Widespread antibiotic resistance has returned attention to bacteriophages as a means of managing bacterial pathogenesis. Synthetic biology approaches to engineer phages have demonstrated genomic editing to broaden natural host ranges, or to optimise microbicidal action. Gram positive pathogens cause serious pastoral animal and human infections that are especially lethal in newborns. Such pathogens are targeted by the obligate lytic phages of the and families. These phages have relatively small ~20 kb linear protein-capped genomes and their compact organisation, relatively few structural elements, and broad host range, are appealing from a phage-engineering standpoint. In this study, we focus on portal proteins, which are core elements for the assembly of such tailed phages. The structures of dodecameric portal complexes from phage GA1, which targets , and phage phiCPV4 that infects , were determined at resolutions of 3.3 Å and 2.9 Å, respectively. Both are found to closely resemble the related phi29 portal protein fold. However, the portal protein of phiCPV4 exhibits interesting differences in the clip domain. These structures provide new insights on structural diversity in portal proteins and will be essential for considerations in phage structural engineering. | |||||||||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 10.2 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 13.8 KB 13.8 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 10.5 KB | Display | ![]() |
Images | ![]() | 98.2 KB | ||
Filedesc metadata | ![]() | 5.8 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 425.4 KB | Display | ![]() |
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Full document | ![]() | 424.9 KB | Display | |
Data in XML | ![]() | 11.3 KB | Display | |
Data in CIF | ![]() | 15.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7pv4MC ![]() 7pv2C M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Map
File | ![]() | ||||||||||||||||||||
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Voxel size | X=Y=Z: 1.07 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
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Sample components
-Entire : PhiCPV4 phage portal protein
Entire | Name: PhiCPV4 phage portal protein |
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Components |
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-Supramolecule #1: PhiCPV4 phage portal protein
Supramolecule | Name: PhiCPV4 phage portal protein / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: Dodecamer complex made up of 12 subunits. |
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Source (natural) | Organism: ![]() ![]() |
-Macromolecule #1: Connector protein
Macromolecule | Name: Connector protein / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 34.652238 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MSKRKSYWNQ GDKILLKNDV FMVDRYYDYY SNMGLNRFRW KNLPPGMESR HIEQALFNEG QAVFFKNTDP NEPYGFLCLP CAPSNGQNI YGDPVDFNGI GVNKYFTNLS PLNAVRILDN DNGLAPVRHI AYYTYLMSQI EMTINMNLDQ QKFPIIIGAT Q KNKLSMEN ...String: MSKRKSYWNQ GDKILLKNDV FMVDRYYDYY SNMGLNRFRW KNLPPGMESR HIEQALFNEG QAVFFKNTDP NEPYGFLCLP CAPSNGQNI YGDPVDFNGI GVNKYFTNLS PLNAVRILDN DNGLAPVRHI AYYTYLMSQI EMTINMNLDQ QKFPIIIGAT Q KNKLSMEN LYEKYSSFEP NILVDEKLAQ ALQEGKGFDA LNTQAPYLLD KLADFKKTCE NELLTFLGIN NTNNDKRERL LT DEVNANN SQITFVLEMA YKNRLDACKR INEMFGLNLE VEKVVNLLEV DMKGDVKNEG INGE UniProtKB: Connector protein |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 0.05 mg/mL |
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Buffer | pH: 7.5 |
Grid | Model: PELCO Ultrathin Carbon with Lacey Carbon / Material: COPPER / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281 K / Instrument: FEI VITROBOT MARK IV Details: 3 ul of sample was applied to lacey carbon grids.. |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Temperature | Min: 95.0 K / Max: 98.0 K |
Specialist optics | Energy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3838 pixel / Digitization - Dimensions - Height: 3710 pixel / Digitization - Frames/image: 1-12 / Number grids imaged: 1 / Number real images: 2903 / Average electron dose: 1.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.2 µm |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: AB INITIO MODEL / Overall B value: 74.6 |
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Output model | ![]() PDB-7pv4: |