+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-19281 | |||||||||
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Title | Bacteriophage JBD30 empty particle capsid | |||||||||
Map data | main map | |||||||||
Sample |
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Keywords | bacteriophage JBD30 / virion / capsid / empty particle / VIRUS | |||||||||
Function / homology | Bacteriophage Mu, GpT / Mu-like prophage major head subunit gpT / Bacteriophage Mu GpT domain-containing protein Function and homology information | |||||||||
Biological species | Pseudomonas phage JBD30 (virus) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.58 Å | |||||||||
Authors | Valentova L / Fuzik T / Plevka P | |||||||||
Funding support | Czech Republic, European Union, 2 items
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Citation | Journal: EMBO J / Year: 2024 Title: Structure and replication of Pseudomonas aeruginosa phage JBD30. Authors: Lucie Valentová / Tibor Füzik / Jiří Nováček / Zuzana Hlavenková / Jakub Pospíšil / Pavel Plevka / Abstract: Bacteriophages are the most abundant biological entities on Earth, but our understanding of many aspects of their lifecycles is still incomplete. Here, we have structurally analysed the infection ...Bacteriophages are the most abundant biological entities on Earth, but our understanding of many aspects of their lifecycles is still incomplete. Here, we have structurally analysed the infection cycle of the siphophage Casadabanvirus JBD30. Using its baseplate, JBD30 attaches to Pseudomonas aeruginosa via the bacterial type IV pilus, whose subsequent retraction brings the phage to the bacterial cell surface. Cryo-electron microscopy structures of the baseplate-pilus complex show that the tripod of baseplate receptor-binding proteins attaches to the outer bacterial membrane. The tripod and baseplate then open to release three copies of the tape-measure protein, an event that is followed by DNA ejection. JBD30 major capsid proteins assemble into procapsids, which expand by 7% in diameter upon filling with phage dsDNA. The DNA-filled heads are finally joined with 180-nm-long tails, which bend easily because flexible loops mediate contacts between the successive discs of major tail proteins. It is likely that the structural features and replication mechanisms described here are conserved among siphophages that utilize the type IV pili for initial cell attachment. #1: Journal: Embo J. / Year: 2024 Title: Structure and replication of Pseudomonas aeruginosa phage JBD30 Authors: Valentova L / Plevka P / Fuzik T / Novacek J / Pospisil J | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_19281.map.gz | 2.1 GB | EMDB map data format | |
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Header (meta data) | emd-19281-v30.xml emd-19281.xml | 20.4 KB 20.4 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_19281_fsc.xml | 29.5 KB | Display | FSC data file |
Images | emd_19281.png | 258.5 KB | ||
Masks | emd_19281_msk_1.map | 2.2 GB | Mask map | |
Filedesc metadata | emd-19281.cif.gz | 6.3 KB | ||
Others | emd_19281_half_map_1.map.gz emd_19281_half_map_2.map.gz | 1.8 GB 1.8 GB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-19281 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-19281 | HTTPS FTP |
-Validation report
Summary document | emd_19281_validation.pdf.gz | 1.3 MB | Display | EMDB validaton report |
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Full document | emd_19281_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | emd_19281_validation.xml.gz | 36 KB | Display | |
Data in CIF | emd_19281_validation.cif.gz | 49.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-19281 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-19281 | HTTPS FTP |
-Related structure data
Related structure data | 8rkoMC 8rk3C 8rk4C 8rk5C 8rk6C 8rk7C 8rk8C 8rk9C 8rkaC 8rkbC 8rkcC 8rknC 8rkxC 8rqeC M: atomic model generated by this map C: citing same article (ref.) |
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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_19281.map.gz / Format: CCP4 / Size: 2.2 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | main map | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.8336 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_19281_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: half map 1
File | emd_19281_half_map_1.map | ||||||||||||
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Annotation | half_map_1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map 2
File | emd_19281_half_map_2.map | ||||||||||||
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Annotation | half_map_2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Pseudomonas phage JBD30
Entire | Name: Pseudomonas phage JBD30 (virus) |
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Components |
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-Supramolecule #1: Pseudomonas phage JBD30
Supramolecule | Name: Pseudomonas phage JBD30 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all Details: Phage JBD30 was propagated in P. aeruginosa strain BAA-28 and purified using CsCl gradient. NCBI-ID: 1223260 / Sci species name: Pseudomonas phage JBD30 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No |
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Host (natural) | Organism: Pseudomonas aeruginosa (bacteria) / Strain: BAA-28 |
Molecular weight | Theoretical: 13.971 MDa |
Virus shell | Shell ID: 1 / Name: JBD30 capsid / Diameter: 640.0 Å / T number (triangulation number): 7 |
-Macromolecule #1: Bacteriophage Mu GpT domain-containing protein
Macromolecule | Name: Bacteriophage Mu GpT domain-containing protein / type: protein_or_peptide / ID: 1 / Number of copies: 7 / Enantiomer: LEVO |
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Source (natural) | Organism: Pseudomonas phage JBD30 (virus) |
Molecular weight | Theoretical: 33.69498 KDa |
Sequence | String: MAIITPALIS ALKTSFQKHF QDALATAPST YLQVATVIPS TTASNTYGWL GQFPKLREWI GQRVIKDMAA QGYQITNKLF ESTVGVKRT DIEDDNLGVY GPLMQEMGRA AGAHPDELVF ALLKAGNANL CYDGQNFFDT DHPVYPNVDG TGTATTVSNL F APAADPGA ...String: MAIITPALIS ALKTSFQKHF QDALATAPST YLQVATVIPS TTASNTYGWL GQFPKLREWI GQRVIKDMAA QGYQITNKLF ESTVGVKRT DIEDDNLGVY GPLMQEMGRA AGAHPDELVF ALLKAGNANL CYDGQNFFDT DHPVYPNVDG TGTATTVSNL F APAADPGA AWYLLDTSRS LKPLIYQERM KPSFTSMTKE DDEQVFMADE YRYGVRSRCN VGFGFWQLAA MSTEELNQVN FE KVYDAMR NQKADGGRPL DIRPNLLVVP TTLRSKAKEV VGVQRLANGA DNPNFELVQV LDTAWLN UniProtKB: Bacteriophage Mu GpT domain-containing 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:
Details: 10 mM MgSO4, 10 mM NaCl, 50 mM Tris pH 8 | ||||||||||||
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Grid | Model: Quantifoil R2/1 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 15 sec. / Pretreatment - Atmosphere: OTHER / Details: Gatan Solaris II | ||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV Details: blotting force 0, blotting time 2 s, waiting time 15 s. | ||||||||||||
Details | phage titer 10^11 PFU |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 10 eV |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number grids imaged: 1 / Number real images: 12356 / Average exposure time: 2.0 sec. / Average electron dose: 34.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 105000 |
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: OTHER |
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Output model | PDB-8rko: |