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Yorodumi- EMDB-4442: Icosahedrally averaged capsid of empty particle of bacteriophage P68 -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-4442 | ||||||||||||
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Title | Icosahedrally averaged capsid of empty particle of bacteriophage P68 | ||||||||||||
Map data | Icosahedraly averaged capsid of the empty particle of bacteriophage P68 | ||||||||||||
Sample |
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Keywords | structural protein / bacteriophage capsid / HK97 fold | ||||||||||||
Function / homology | Uncharacterized protein / Major head protein Function and homology information | ||||||||||||
Biological species | Staphylococcus phage P68 (virus) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.5 Å | ||||||||||||
Authors | Hrebik D / Skubnik K | ||||||||||||
Funding support | Czech Republic, 3 items
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Citation | Journal: Sci Adv / Year: 2019 Title: Structure and genome ejection mechanism of phage P68. Authors: Dominik Hrebík / Dana Štveráková / Karel Škubník / Tibor Füzik / Roman Pantůček / Pavel Plevka / Abstract: Phages infecting can be used as therapeutics against antibiotic-resistant bacterial infections. However, there is limited information about the mechanism of genome delivery of phages that infect ...Phages infecting can be used as therapeutics against antibiotic-resistant bacterial infections. However, there is limited information about the mechanism of genome delivery of phages that infect Gram-positive bacteria. Here, we present the structures of native phage P68, genome ejection intermediate, and empty particle. The P68 head contains 72 subunits of inner core protein, 15 of which bind to and alter the structure of adjacent major capsid proteins and thus specify attachment sites for head fibers. Unlike in the previously studied phages, the head fibers of P68 enable its virion to position itself at the cell surface for genome delivery. The unique interaction of one end of P68 DNA with one of the 12 portal protein subunits is disrupted before the genome ejection. The inner core proteins are released together with the DNA and enable the translocation of phage genome across the bacterial membrane into the cytoplasm. | ||||||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_4442.map.gz | 81 MB | EMDB map data format | |
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Header (meta data) | emd-4442-v30.xml emd-4442.xml | 17.7 KB 17.7 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_4442_fsc.xml | 21.2 KB | Display | FSC data file |
Images | emd_4442.png | 199.1 KB | ||
Filedesc metadata | emd-4442.cif.gz | 6.3 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-4442 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-4442 | HTTPS FTP |
-Validation report
Summary document | emd_4442_validation.pdf.gz | 346.1 KB | Display | EMDB validaton report |
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Full document | emd_4442_full_validation.pdf.gz | 345.3 KB | Display | |
Data in XML | emd_4442_validation.xml.gz | 17 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4442 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4442 | HTTPS FTP |
-Related structure data
Related structure data | 6ib1MC 4435C 4436C 4437C 4438C 4440C 4449C 4450C 4451C 4453C 4454C 4455C 4456C 4457C 4458C 4459C 6iabC 6iacC 6iatC 6iawC 6q3gC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_4442.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Icosahedraly averaged capsid of the empty particle of bacteriophage P68 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.063 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Staphylococcus phage P68
Entire | Name: Staphylococcus phage P68 (virus) |
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Components |
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-Supramolecule #1: Staphylococcus phage P68
Supramolecule | Name: Staphylococcus phage P68 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 204090 / Sci species name: Staphylococcus phage P68 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No |
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Host (natural) | Organism: Staphylococcus aureus (bacteria) / Strain: dTarM 4220 |
Molecular weight | Theoretical: 6.9 KDa |
Virus shell | Shell ID: 1 / Name: Capsid / Diameter: 480.0 Å / T number (triangulation number): 4 |
-Supramolecule #2: Major capsid protein
Supramolecule | Name: Major capsid protein / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1 |
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Source (natural) | Organism: Staphylococcus phage P68 (virus) |
-Supramolecule #3: Arstotzka protein
Supramolecule | Name: Arstotzka protein / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2 |
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Source (natural) | Organism: Staphylococcus phage P68 (virus) |
-Macromolecule #1: Major head protein
Macromolecule | Name: Major head protein / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: Staphylococcus phage P68 (virus) |
Molecular weight | Theoretical: 46.954941 KDa |
Sequence | String: MAQQSTKNET ALLVAKSAKS ALQDFNHDYS KSWTFGDKWD NSNTMFETFV NKYLFPKINE TLLIDIALGN RFNWLAKEQD FIGQYSEEY VIMDTVPINM DLSKNEELML KRNYPRMATK LYGNGIVKKQ KFTLNNNDTR FNFQTLADAT NYALGVYKKK I SDINVLEE ...String: MAQQSTKNET ALLVAKSAKS ALQDFNHDYS KSWTFGDKWD NSNTMFETFV NKYLFPKINE TLLIDIALGN RFNWLAKEQD FIGQYSEEY VIMDTVPINM DLSKNEELML KRNYPRMATK LYGNGIVKKQ KFTLNNNDTR FNFQTLADAT NYALGVYKKK I SDINVLEE KEMRAMLVDY SLNQLSETNV RKATSKEDLA SKVFEAILNL QNNSAKYNEV HRASGGAIGQ YTTVSKLKDI VI LTTDSLK SYLLDTKIAN TFQIAGIDFT DHVISFDDLG GVFKVTKEFK LQNQDSIDFL RAYGDYQSQL GDTIPVGAVF TYD VSKLKE FTGNVEEIKP KSDLYAFILD INSIKYKRYT KGMLKPPFHN PEFDEVTHWI HYYSFKAISP FFNKILITDQ DVNP KPEEE LQE UniProtKB: Major head protein |
-Macromolecule #2: Uncharacterized protein
Macromolecule | Name: Uncharacterized protein / type: protein_or_peptide / ID: 2 Details: MYEGNNMRSMMGTSYEDSRLNKRTELNENMSIDTNKSEDSYGVQIHSLSKQSFTGDVEEE Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: Staphylococcus phage P68 (virus) |
Molecular weight | Theoretical: 6.922464 KDa |
Sequence | String: MYEGNNMRSM MGTSYEDSRL NKRTELNENM SIDTNKSEDS YGVQIHSLSK QSFTGDVEEE UniProtKB: Uncharacterized protein |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 2 mg/mL | ||||||||||||
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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: NITROGEN | ||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 293 K / Instrument: FEI VITROBOT MARK IV / Details: blot time 2s; blot force -2; 3.6 ul of sample. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON II (4k x 4k) / Detector mode: INTEGRATING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Digitization - Frames/image: 1-7 / Number grids imaged: 2 / Number real images: 2891 / Average exposure time: 1.0 sec. / Average electron dose: 21.0 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: 0.003 µm / Nominal defocus min: 0.001 µm / Nominal magnification: 75000 |
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
Initial model | PDB ID: Chain - Source name: PDB / Chain - Initial model type: experimental model |
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Details | Reconstruction of the native P68 capsid was used as initial model |
Refinement | Space: REAL / Protocol: AB INITIO MODEL |
Output model | PDB-6ib1: |