+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-19270 | |||||||||
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Title | Capsid of bacteriophage JBD30 decorated with minor capsid protein trimers computed in I4 symmetry | |||||||||
Map data | main map | |||||||||
Sample |
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Keywords | bacteriophage JBD30 / virion / capsid / minor capsid protein / major capsid protein / VIRUS | |||||||||
Function / homology | Bacteriophage Mu, GpT / Mu-like prophage major head subunit gpT / Bacteriophage Mu GpT domain-containing protein / Mu-like prophage FluMu N-terminal domain-containing protein Function and homology information | |||||||||
Biological species | Pseudomonas phage JBD30 (virus) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.95 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_19270.map.gz | 2.1 GB | EMDB map data format | |
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Header (meta data) | emd-19270-v30.xml emd-19270.xml | 20.2 KB 20.2 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_19270_fsc.xml | 29.5 KB | Display | FSC data file |
Images | emd_19270.png | 273.2 KB | ||
Masks | emd_19270_msk_1.map | 2.2 GB | Mask map | |
Filedesc metadata | emd-19270.cif.gz | 6.3 KB | ||
Others | emd_19270_half_map_1.map.gz emd_19270_half_map_2.map.gz | 1.8 GB 1.8 GB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-19270 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-19270 | HTTPS FTP |
-Related structure data
Related structure data | 8rkcMC 19256 19257 19258 19259 19260 19261 19262 19263 19264 19265 19266 19267 19268 19269 19271 19272 19273 19274 19280 19281 19285 19439 19561 8rk3C 8rk4C 8rk5C 8rk6C 8rk7C 8rk8C 8rk9C 8rkaC 8rkbC 8rknC 8rkoC 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_19270.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_19270_msk_1.map | ||||||||||||
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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: 19.052 MDa |
Virus shell | Shell ID: 1 / Name: JBD30 capsid / Diameter: 640.0 Å / T number (triangulation number): 7 |
-Macromolecule #1: Mu-like prophage FluMu N-terminal domain-containing protein
Macromolecule | Name: Mu-like prophage FluMu N-terminal 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: 12.112113 KDa |
Sequence | String: MARQNSAAKT TAKSKTDPAT EKPKDDTLPD STDDASPTAP ETPATKPDSA SDEVEGVFVR ATVERRCRAG FCFDKEGQGF ADGVLSDEQ LEALESDPLL KVERCTFSGN QEGE UniProtKB: Mu-like prophage FluMu N-terminal domain-containing protein |
-Macromolecule #2: Bacteriophage Mu GpT domain-containing protein
Macromolecule | Name: Bacteriophage Mu GpT domain-containing protein / type: protein_or_peptide / ID: 2 / 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 Solarus II | ||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV | ||||||||||||
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 |
+Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: OTHER |
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Output model | PDB-8rkc: |