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Open data
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Basic information
Entry | ![]() | |||||||||
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Title | Procapsid of bacteriophage JBD30 computed in I4 symmetry | |||||||||
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![]() | bacteriophage / virion / procapsid / VIRUS | |||||||||
Function / homology | Bacteriophage Mu, GpT / Mu-like prophage major head subunit gpT / Bacteriophage Mu GpT domain-containing protein![]() | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.01 Å | |||||||||
![]() | Valentova L / Fuzik T / Plevka P | |||||||||
Funding support | European Union, ![]()
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![]() | ![]() 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 | ![]() | 1.3 GB | ![]() | |
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Header (meta data) | ![]() ![]() | 19.1 KB 19.1 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 25.5 KB | Display | ![]() |
Images | ![]() | 257 KB | ||
Masks | ![]() | 1.4 GB | ![]() | |
Filedesc metadata | ![]() | 6.1 KB | ||
Others | ![]() ![]() | 1.1 GB 1.1 GB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8rkxMC ![]() 19256 ![]() 19257 ![]() 19258 ![]() 19259 ![]() 19260 ![]() 19261 ![]() 19262 ![]() 19263 ![]() 19264 ![]() 19265 ![]() 19266 ![]() 19267 ![]() 19268 ![]() 19269 ![]() 19270 ![]() 19271 ![]() 19272 ![]() 19273 ![]() 19274 ![]() 19280 ![]() 19281 ![]() 19439 ![]() 19561 ![]() 8rk3C ![]() 8rk4C ![]() 8rk5C ![]() 8rk6C ![]() 8rk7C ![]() 8rk8C ![]() 8rk9C ![]() 8rkaC ![]() 8rkbC ![]() 8rkcC ![]() 8rknC ![]() 8rkoC ![]() 8rqeC M: atomic model generated by this map C: citing same article ( |
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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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Voxel size | X=Y=Z: 1.057 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
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Projections & Slices |
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Density Histograms |
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Sample components
-Entire : Pseudomonas phage JBD30
Entire | Name: ![]() |
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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: ![]() ![]() |
Molecular weight | Theoretical: 13.971 MDa |
Virus shell | Shell ID: 1 / Name: JBD30 procapsid / Diameter: 570.0 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: ![]() |
Molecular weight | Theoretical: 33.492707 KDa |
Sequence | String: IITPALISAL KTSFQKHFQD ALATAPSTYL QVATVIPSTT ASNTYGWLGQ FPKLREWIGQ RVIKDMAAQG YQITNKLFES TVGVKRTDI EDDNLGVYGP LMQEMGRAAG AHPDELVFAL LKAGNANLCY DGQNFFDTDH PVYPNVDGTG TATTVSNLFA P AADPGAAW ...String: IITPALISAL KTSFQKHFQD ALATAPSTYL QVATVIPSTT ASNTYGWLGQ FPKLREWIGQ RVIKDMAAQG YQITNKLFES TVGVKRTDI EDDNLGVYGP LMQEMGRAAG AHPDELVFAL LKAGNANLCY DGQNFFDTDH PVYPNVDGTG TATTVSNLFA P AADPGAAW YLLDTSRSLK PLIYQERMKP SFTSMTKEDD EQVFMADEYR YGVRSRCNVG FGFWQLAAMS TEELNQVNFE KV YDAMRNQ KADGGRPLDI RPNLLVVPTT LRSKAKEVVG VQRLANGADN PNFELVQVLD TAWLN UniProtKB: Bacteriophage Mu GpT domain-containing protein |
-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:
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 |
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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: 1-40 / Number grids imaged: 1 / Number real images: 13769 / Average exposure time: 7.5 sec. / Average electron dose: 53.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
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 |
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Image processing
-Atomic model buiding 1
Details | de novo model building |
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Refinement | Space: REAL / Protocol: OTHER |
Output model | ![]() PDB-8rkx: |