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Yorodumi- EMDB-19269: Capsid of bacteriophage JBD30 decorated with minor capsid protein... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-19269 | |||||||||
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Title | Capsid of bacteriophage JBD30 decorated with minor capsid protein trimers - asymmetric reconstruction | |||||||||
Map data | main_map | |||||||||
Sample |
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Keywords | bacteriophage JBD30 / virion / capsid / minor capsid protein / VIRUS | |||||||||
Biological species | Pseudomonas phage JBD30 (virus) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 18.59 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: 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_19269.map.gz | 191.5 MB | EMDB map data format | |
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Header (meta data) | emd-19269-v30.xml emd-19269.xml | 17.6 KB 17.6 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_19269_fsc.xml | 30.2 KB | Display | FSC data file |
Images | emd_19269.png | 52.9 KB | ||
Masks | emd_19269_msk_1.map | 2.2 GB | Mask map | |
Filedesc metadata | emd-19269.cif.gz | 4.8 KB | ||
Others | emd_19269_half_map_1.map.gz emd_19269_half_map_2.map.gz | 1.8 GB 1.8 GB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-19269 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-19269 | HTTPS FTP |
-Validation report
Summary document | emd_19269_validation.pdf.gz | 1 MB | Display | EMDB validaton report |
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Full document | emd_19269_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | emd_19269_validation.xml.gz | 37.2 KB | Display | |
Data in CIF | emd_19269_validation.cif.gz | 50.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-19269 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-19269 | HTTPS FTP |
-Related structure data
Related structure data | 8rk3C 8rk4C 8rk5C 8rk6C 8rk7C 8rk8C 8rk9C 8rkaC 8rkbC 8rkcC 8rknC 8rkoC 8rkxC 8rqeC C: citing same article (ref.) |
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-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_19269.map.gz / Format: CCP4 / Size: 2.2 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | main_map | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.04 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_19269_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: half map 1
File | emd_19269_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_19269_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 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: 19.052 MDa |
Virus shell | Shell ID: 1 / Name: JBD30 capsid decorated with minor capsid porteins / Diameter: 640.0 Å / T number (triangulation number): 7 |
-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 Solarus 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 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: 1-25 / Number grids imaged: 1 / Number real images: 11300 / Average exposure time: 5.0 sec. / Average electron dose: 30.0 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: 130000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |