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Yorodumi- EMDB-4440: Structure of head fiber and inner core protein gp22 of native bac... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-4440 | ||||||||||||
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Title | Structure of head fiber and inner core protein gp22 of native bacteriophage P68 | ||||||||||||
Map data | Map of head fiber and gp22 bound to hexon adjacent to portal, masked from five-fold cryoEM reconstruction of native bacteriophage P68 capsid | ||||||||||||
Sample |
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Keywords | structural protein / bacteriophage / head fiber / inner core protein | ||||||||||||
Function / homology | Uncharacterized protein / Major head protein Function and homology information | ||||||||||||
Biological species | Staphylococcus phage P68 (virus) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.8 Å | ||||||||||||
Authors | Hrebik D / Skubnik K / Fuzik T / Plevka P | ||||||||||||
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_4440.map.gz | 2 MB | EMDB map data format | |
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Header (meta data) | emd-4440-v30.xml emd-4440.xml | 19.5 KB 19.5 KB | Display Display | EMDB header |
Images | emd_4440.png | 81.1 KB | ||
Filedesc metadata | emd-4440.cif.gz | 6.9 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-4440 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-4440 | HTTPS FTP |
-Related structure data
Related structure data | 6iawMC 4435C 4436C 4437C 4438C 4442C 4449C 4450C 4451C 4453C 4454C 4455C 4456C 4457C 4458C 4459C 6iabC 6iacC 6iatC 6ib1C 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_4440.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Map of head fiber and gp22 bound to hexon adjacent to portal, masked from five-fold cryoEM reconstruction of native bacteriophage P68 capsid | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 19.7 MDa |
Virus shell | Shell ID: 1 / Name: Capsid / Diameter: 480.0 Å / T number (triangulation number): 4 |
-Macromolecule #1: Major head protein
Macromolecule | Name: Major head protein / type: protein_or_peptide / ID: 1 / Number of copies: 6 / 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: Arstotzka protein
Macromolecule | Name: Arstotzka protein / type: protein_or_peptide / ID: 2 / Number of copies: 6 / 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 |
-Macromolecule #3: Head fiber
Macromolecule | Name: Head fiber / type: protein_or_peptide / ID: 3 Details: Poly alanine chain fitted to the density of head-fiber Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Staphylococcus phage P68 (virus) |
Molecular weight | Theoretical: 5.720042 KDa |
Sequence | String: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) ...String: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK) |
-Macromolecule #4: inner core protein
Macromolecule | Name: inner core protein / type: protein_or_peptide / ID: 4 Details: Poly alanine chain fitted to the density of the inner core protein bound to hexon adjacent to portal Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Staphylococcus phage P68 (virus) |
Molecular weight | Theoretical: 3.507314 KDa |
Sequence | String: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) |
-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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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 FIELDBright-field microscopy / 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 |
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 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Particle selection | Number selected: 37218 |
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Startup model | Type of model: EMDB MAP EMDB ID: Details: The initial model was scaled and clipped in EMAN2 to match the dimensions of phage P68. command: e2proc3d.py --clip=600 --scale=0.73 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2.1) |
Final 3D classification | Number classes: 3 / Avg.num./class: 11210 / Software - Name: RELION (ver. 2.1) |
Final angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2.1) |
Final reconstruction | Number classes used: 1 / Applied symmetry - Point group: C5 (5 fold cyclic) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.1) / Number images used: 28826 |
-Atomic model buiding 1
Initial model | PDB ID: Chain - Source name: PDB / Chain - Initial model type: experimental model |
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Details | The refinement was conducted on rigid body fitted major capsid proteins and Arstotzka proteins obtained from related structure of 6IAT; EMD-4438. The chains were fitted into hexon adjacent to portal of P68 capsid obtained from 5-fold symmetrized reconstruction. Subsequently, poly-alanine chains were manually built into densities corresponding to N-terminal part of head-fiber (chain IDs H,K,L) and C-terminal part of inner core protein (chain IDs X,Y,Z). The map was masked according to the related pdb in chimera, normalized and put into several rounds of a real space refinement in Phenix. |
Refinement | Space: REAL / Protocol: AB INITIO MODEL |
Output model | PDB-6iaw: |