+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-14909 | |||||||||
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Title | Tail needle of bacteriophage SU10 | |||||||||
Map data | ||||||||||
Sample |
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Keywords | bacteriophage / tail / tail needle / VIRUS | |||||||||
Biological species | Escherichia coli (E. coli) / Escherichia phage vB_EcoP_SU10 (virus) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 10.0 Å | |||||||||
Authors | Siborova M / Fuzik T / Prochazkova M / Novacek J / Plevka P | |||||||||
Funding support | Czech Republic, 1 items
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Citation | Journal: Nat Commun / Year: 2022 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 | emd_14909.map.gz | 80.5 MB | EMDB map data format | |
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Header (meta data) | emd-14909-v30.xml emd-14909.xml | 19.2 KB 19.2 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_14909_fsc.xml | 10.7 KB | Display | FSC data file |
Images | emd_14909.png | 39.1 KB | ||
Filedesc metadata | emd-14909.cif.gz | 5.1 KB | ||
Others | emd_14909_half_map_1.map.gz emd_14909_half_map_2.map.gz | 80.8 MB 80.8 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-14909 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-14909 | HTTPS FTP |
-Validation report
Summary document | emd_14909_validation.pdf.gz | 645.6 KB | Display | EMDB validaton report |
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Full document | emd_14909_full_validation.pdf.gz | 645.2 KB | Display | |
Data in XML | emd_14909_validation.xml.gz | 17.8 KB | Display | |
Data in CIF | emd_14909_validation.cif.gz | 23.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-14909 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-14909 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_14909.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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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: #1
File | emd_14909_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_14909_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Escherichia phage vB_EcoP_SU10
Entire | Name: Escherichia phage vB_EcoP_SU10 (virus) |
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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 / Details: NCBI taxonomy ID: 1519788 / 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: Escherichia coli (E. coli) |
Molecular weight | Theoretical: 105.8 kDa/nm |
Virus shell | Shell ID: 1 / Name: Tail needle |
-Macromolecule #1: Tail Needle
Macromolecule | Name: Tail Needle / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Escherichia coli (E. coli) |
Sequence | String: MGAGGFRKNT GRNNTTLPYN VGFLNNVQDT ETYNVAVYDE LQKV STATN QMFQAIDEIH EEIDVRIKAL NAMNLQFDEL ENRITTEIET AIADIQTQMG NLS TEDIWD NSVQPPVKLE STVSGFKTSI EGNTTKIQTV EGIVNDQGQE IALVQTELQN IN GSLSQYM ...String: MGAGGFRKNT GRNNTTLPYN VGFLNNVQDT ETYNVAVYDE LQKV STATN QMFQAIDEIH EEIDVRIKAL NAMNLQFDEL ENRITTEIET AIADIQTQMG NLS TEDIWD NSVQPPVKLE STVSGFKTSI EGNTTKIQTV EGIVNDQGQE IALVQTELQN IN GSLSQYM KLSEYEATWG VNSTVNGRYA GVKLTNNGTN SQFQVTANKF IVGDGSSGNT P FVFEGGRA RMEFADIKNV NITTAQIANA RIQWAQIDNV SISNAQIQNL SADKITAGSM WGSNWRLTV GGDFVMGGTG GAQLWMNGNR IDFYDGSGAL RIRIGSW GENBANK: GENBANK: NC_027395.1 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 Component:
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Grid | Model: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: OTHER | ||||||||||||
Vitrification | Cryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV | ||||||||||||
Details | PFU 10^11 |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON III (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: FIELD EMISSION GUN |
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 |