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Open data
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Basic information
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Title | Capsid structure of the Cyanophage P-SCSP1u | |||||||||
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![]() | Whole virus / ![]() ![]() ![]() | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Liu H / Dang S | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Cryo-EM structure of cyanophage P-SCSP1u offers insights into DNA gating and evolution of T7-like viruses. Authors: Lanlan Cai / Hang Liu / Wen Zhang / Shiwei Xiao / Qinglu Zeng / Shangyu Dang / ![]() Abstract: Cyanophages, together with their host cyanobacteria, play important roles in marine biogeochemical cycles and control of marine food webs. The recently identified MPP-C (Marine Picocyanobacteria ...Cyanophages, together with their host cyanobacteria, play important roles in marine biogeochemical cycles and control of marine food webs. The recently identified MPP-C (Marine Picocyanobacteria Podovirus clade C) cyanophages, belonging to the T7-like podoviruses, contain the smallest genomes among cyanopodoviruses and exhibit distinct infection kinetics. However, understanding of the MPP-C cyanophage infection process is hindered by the lack of high-resolution structural information. Here, we report the cryo-EM structure of the cyanophage P-SCSP1u, a representative member of the MPP-C phages, in its native form at near-atomic resolution, which reveals the assembly mechanism of the capsid and molecular interaction of the portal-tail complex. Structural comparison of the capsid proteins of P-SCSP1u and other podoviruses with known structures provides insights into the evolution of T7-like viruses. Furthermore, our study provides the near-atomic resolution structure of portal-tail complex for T7-like viruses. On the basis of previously reported structures of phage T7, we identify an additional valve and gate to explain the DNA gating mechanism for the T7-like viruses. | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 227 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 14.2 KB 14.2 KB | Display Display | ![]() |
Images | ![]() | 99.8 KB | ||
Masks | ![]() | 244.1 MB | ![]() | |
Filedesc metadata | ![]() | 5.2 KB | ||
Others | ![]() ![]() | 194.4 MB 194.4 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
EMDB pages | ![]() ![]() |
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Map
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Voxel size | X=Y=Z: 0.85 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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Density Histograms |
-Half map: #2
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Projections & Slices |
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Density Histograms |
-Half map: #1
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Density Histograms |
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Sample components
-Entire : Prochlorococcus phage P-SCSP1u
Entire | Name: ![]() |
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Components |
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-Supramolecule #1: Prochlorococcus phage P-SCSP1u
Supramolecule | Name: Prochlorococcus phage P-SCSP1u / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 2914505 / Sci species name: Prochlorococcus phage P-SCSP1u / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No |
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Host (natural) | Organism: ![]() ![]() |
-Macromolecule #1: The capsid protein(gp 19) of P-SCSP1u
Macromolecule | Name: The capsid protein(gp 19) of P-SCSP1u / type: protein_or_peptide / ID: 1 / Number of copies: 7 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 35.160438 KDa |
Sequence | String: MANFTPSRLG LVNNTGTGVK DLFLKTFAGE VLSAFRKATI FEDLHTVRTI SSGKSAQFPI VGLSSTSYHS PGTQLTGNAI KHAEAVINI DDKLVSNVFI ADVDEAMNHY DVRSQYSVQM GNALAYTFDQ NVAAMIAQAA RTSTNPNTDL PGGTRIKILK S GTANTAAA ...String: MANFTPSRLG LVNNTGTGVK DLFLKTFAGE VLSAFRKATI FEDLHTVRTI SSGKSAQFPI VGLSSTSYHS PGTQLTGNAI KHAEAVINI DDKLVSNVFI ADVDEAMNHY DVRSQYSVQM GNALAYTFDQ NVAAMIAQAA RTSTNPNTDL PGGTRIKILK S GTANTAAA VAAVTGTDLA TALFSAAEQM DINNLPEEDR YCAIDPTNYY KLVQNTTVIN RDFGGRGAYA EGEVLKVAGI HI VKSNHLP KTNRSAATGE NNTYHANYTD NIGLVFNKQA VGTVKLMDLK MEQTGADIHA LYQGTFMVGS MMHGSGVLRP DCA IELYAA NS |
-Experimental details
-Structure determination
Method | ![]() |
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Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.4 |
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Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD![]() |
Sample stage | Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average exposure time: 4.5 sec. / Average electron dose: 50.0 e/Å2 |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Startup model | Type of model: INSILICO MODEL |
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Initial angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 2.15) |
Final angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 2.15) |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.23 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 2.15) / Number images used: 732864 |