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Open data
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Basic information
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Title | The capsid of bacteriophage SU10. | |||||||||
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Function / homology | Protein of unknown function DUF5309 / Family of unknown function (DUF5309) / Major head protein![]() | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.2 Å | |||||||||
![]() | Siborova M / Fuzik T / Prochazkova M / Novacek J / Plevka P | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Tail proteins of phage SU10 reorganize into the nozzle for genome delivery. Authors: Marta Šiborová / Tibor Füzik / Michaela Procházková / Jiří Nováček / Martin Benešík / Anders S Nilsson / Pavel Plevka / ![]() ![]() Abstract: Escherichia coli phage SU10 belongs to the genus Kuravirus from the class Caudoviricetes of phages with short non-contractile tails. In contrast to other short-tailed phages, the tails of Kuraviruses ...Escherichia coli phage SU10 belongs to the genus Kuravirus from the class Caudoviricetes of phages with short non-contractile tails. In contrast to other short-tailed phages, the tails of Kuraviruses elongate upon cell attachment. Here we show that the virion of SU10 has a prolate head, containing genome and ejection proteins, and a tail, which is formed of portal, adaptor, nozzle, and tail needle proteins and decorated with long and short fibers. The binding of the long tail fibers to the receptors in the outer bacterial membrane induces the straightening of nozzle proteins and rotation of short tail fibers. After the re-arrangement, the nozzle proteins and short tail fibers alternate to form a nozzle that extends the tail by 28 nm. Subsequently, the tail needle detaches from the nozzle proteins and five types of ejection proteins are released from the SU10 head. The nozzle with the putative extension formed by the ejection proteins enables the delivery of the SU10 genome into the bacterial cytoplasm. It is likely that this mechanism of genome delivery, involving the formation of the tail nozzle, is employed by all Kuraviruses. | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 638.6 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 19.7 KB 19.7 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 45.6 KB | Display | ![]() |
Images | ![]() | 73.1 KB | ||
Others | ![]() ![]() | 6.7 GB 6.7 GB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7z49MC ![]() 7z44C ![]() 7z45C ![]() 7z46C ![]() 7z47C ![]() 7z48C ![]() 7z4aC ![]() 7z4bC ![]() 7z4fC C: citing same article ( M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Map
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.38 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_14488_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_14488_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
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Sample components
-Entire : Escherichia phage vB_EcoP_SU10
Entire | Name: ![]() |
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Components |
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-Supramolecule #1: Escherichia phage vB_EcoP_SU10
Supramolecule | Name: Escherichia phage vB_EcoP_SU10 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 1519788 / Sci species name: Escherichia phage vB_EcoP_SU10 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No |
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Host (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 27.6 MDa |
-Macromolecule #1: Major head protein
Macromolecule | Name: Major head protein / type: protein_or_peptide / ID: 1 / Number of copies: 95 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 38.616457 KDa |
Sequence | String: MANPTLFVSY DQNGKKLSFA NWISVLSPQD TPFVSMTGKE SINQTIFSWQ TDALASVDGN NAHVEGSRAE DGEMKPTVIK SNVTQILRK VVRVSDTANT TANYGRGREL MYQLEKKGKE IKRDLEKILL SGQARTDVLA DQYLTNSAAD PAVAGLNDTH A ARKTGAFQ ...String: MANPTLFVSY DQNGKKLSFA NWISVLSPQD TPFVSMTGKE SINQTIFSWQ TDALASVDGN NAHVEGSRAE DGEMKPTVIK SNVTQILRK VVRVSDTANT TANYGRGREL MYQLEKKGKE IKRDLEKILL SGQARTDVLA DQYLTNSAAD PAVAGLNDTH A ARKTGAFQ FLCAHGGLAG GVVDKTKNGP ADPDTGAVTV KVAQNASNPT TNIGFDEADI FDMTLQLYTA GSEADIIMIN PA HAKIFAG LQENTQGSRK RIFENTKQFI YEVNSITDPL GQSYKIIVNR WMPTDAVYFF RSADWTQMVL RAPKRTELAK DGS YEKWMI EMEVGLRHRN PYASGVLFTA AGKAAA |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 8 Component:
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Grid | Model: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: OTHER | ||||||||||||
Vitrification | Cryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV | ||||||||||||
Details | PFU 10^11 |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON II (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Average exposure time: 1.0 sec. / Average electron dose: 49.0 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: 2.7 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 59000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
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 |
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Output model | ![]() PDB-7z49: |