+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-14484 | |||||||||
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Title | Central part (C10) of bacteriophage SU10 capsid | |||||||||
Map data | ||||||||||
Sample |
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Keywords | bacteriophage / portal / VIRUS | |||||||||
Function / homology | Protein of unknown function DUF5309 / Family of unknown function (DUF5309) / Major head protein Function and homology information | |||||||||
Biological species | Escherichia phage vB_EcoP_SU10 (virus) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.5 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_14484.map.gz | 88.9 MB | EMDB map data format | |
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Header (meta data) | emd-14484-v30.xml emd-14484.xml | 20.4 KB 20.4 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_14484_fsc.xml | 18 KB | Display | FSC data file |
Images | emd_14484.png | 268.3 KB | ||
Filedesc metadata | emd-14484.cif.gz | 6 KB | ||
Others | emd_14484_half_map_1.map.gz emd_14484_half_map_2.map.gz | 407 MB 407.1 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-14484 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-14484 | HTTPS FTP |
-Validation report
Summary document | emd_14484_validation.pdf.gz | 978 KB | Display | EMDB validaton report |
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Full document | emd_14484_full_validation.pdf.gz | 977.5 KB | Display | |
Data in XML | emd_14484_validation.xml.gz | 26.2 KB | Display | |
Data in CIF | emd_14484_validation.cif.gz | 35.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-14484 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-14484 | HTTPS FTP |
-Related structure data
Related structure data | 7z45MC 7z44C 7z46C 7z47C 7z48C 7z49C 7z4aC 7z4bC 7z4fC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_14484.map.gz / Format: CCP4 / Size: 512 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: #2
File | emd_14484_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_14484_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 / 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: 9.257 MDa |
-Macromolecule #1: Major head protein
Macromolecule | Name: Major head protein / type: protein_or_peptide / ID: 1 / Number of copies: 24 / Enantiomer: LEVO |
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Source (natural) | Organism: Escherichia phage vB_EcoP_SU10 (virus) |
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 UniProtKB: Major head protein |
-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 / 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 |
-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 |
+Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: AB INITIO MODEL |
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Output model | PDB-7z45: |