+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-35174 | |||||||||
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Title | Capsid structure of the Cyanophage P-SCSP1u | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Whole virus / Capsid / cyanophage / T7-like virus / VIRUS | |||||||||
Biological species | Prochlorococcus phage P-SCSP1u (virus) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.23 Å | |||||||||
Authors | Liu H / Dang S | |||||||||
Funding support | Hong Kong, 1 items
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Citation | Journal: Nat Commun / Year: 2023 Title: Cryo-EM structure of cyanophage P-SCSP1u offers insights into DNA gating and evolution of T7-like viruses Authors: Cai L / Liu H / Zhang W / Xiao S / Zeng Q / Dang S | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_35174.map.gz | 227 MB | EMDB map data format | |
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Header (meta data) | emd-35174-v30.xml emd-35174.xml | 14 KB 14 KB | Display Display | EMDB header |
Images | emd_35174.png | 99.8 KB | ||
Masks | emd_35174_msk_1.map | 244.1 MB | Mask map | |
Filedesc metadata | emd-35174.cif.gz | 5.2 KB | ||
Others | emd_35174_half_map_1.map.gz emd_35174_half_map_2.map.gz | 194.4 MB 194.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-35174 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-35174 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_35174.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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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
File | emd_35174_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_35174_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_35174_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Prochlorococcus phage P-SCSP1u
Entire | Name: Prochlorococcus phage P-SCSP1u (virus) |
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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: Prochlorococcus (bacteria) |
-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: Prochlorococcus phage P-SCSP1u (virus) |
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 | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
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Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 81000 |
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 |
-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 |