Dominik Hrebík / Dana Štveráková / Karel Škubník / Tibor Füzik / Roman Pantůček / Pavel Plevka /
PubMed 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.
EMDB-4442, PDB-6ib1: Icosahedrally averaged capsid of empty particle of bacteriophage P68 Method: EM (single particle) / Resolution: 3.5 Å
EMDB-4449: Localized reconstruction of tailknob of native bacteriophage P68 Method: EM (single particle) / Resolution: 11.3 Å
EMDB-4450: Localized reconstruction of tail-spike of bacteriophage P68 Method: EM (single particle) / Resolution: 7.4 Å
EMDB-4451: Icosahedrally averaged genome release intermediate capsid of bacteriophage P68 Method: EM (single particle) / Resolution: 6.3 Å
EMDB-4453: Five-fold averaged reconstruction of the genome release intermediate bacteriophage P68 Method: EM (single particle) / Resolution: 22.7 Å
EMDB-4454: Dodecameric reconstruction of portal and tail of genome release intermediate state of bacteriophage P68 Method: EM (single particle) / Resolution: 18.8 Å
EMDB-4455: Dodecameric reconstruction of portal and tail of genome release intermediate state of bacteriophage P68 (subset with tailknob) Method: EM (single particle) / Resolution: 22.7 Å
EMDB-4456: Five-fold symmetric reconstruction of empty particle of bacteriophage P68 Method: EM (single particle) / Resolution: 4.28 Å
EMDB-4457: Dodecameric reconstruction of portal and tail of empty particle of bacteriophage P68 (subset without tailknob) Method: EM (single particle) / Resolution: 7.1 Å
EMDB-4458: Dodecameric reconstruction of portal and tail of empty partice of bacteriophage P68 (subset with tailknob) Method: EM (single particle) / Resolution: 21.7 Å
In the structure databanks used in Yorodumi, some data are registered as the other names, "COVID-19 virus" and "2019-nCoV". Here are the details of the virus and the list of structure data.
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)
EMDB accession codes are about to change! (news from PDBe EMDB page)
The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
The EM Navigator/Yorodumi systems omit the EMD- prefix.
Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator