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- EMDB-35174: Capsid structure of the Cyanophage P-SCSP1u -

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Basic information

Entry
Database: EMDB / ID: EMD-35174
TitleCapsid structure of the Cyanophage P-SCSP1u
Map data
Sample
  • Virus: Prochlorococcus phage P-SCSP1u (virus)
    • Protein or peptide: The capsid protein(gp 19) of P-SCSP1u
KeywordsWhole virus / Capsid / cyanophage / T7-like virus / VIRUS
Biological speciesProchlorococcus phage P-SCSP1u (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.23 Å
AuthorsLiu H / Dang S
Funding support Hong Kong, 1 items
OrganizationGrant numberCountry
The University Grants Committee, Research Grants Council (RGC) Hong Kong
CitationJournal: Nat Commun / Year: 2023
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
DepositionJan 19, 2023-
Header (metadata) releaseOct 25, 2023-
Map releaseOct 25, 2023-
UpdateMay 8, 2024-
Current statusMay 8, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_35174.png

Downloads & links

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Map

FileDownload / File: emd_35174.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 400 pix.
= 340. Å		0.85 Å/pix.
x 400 pix.
= 340. Å		0.85 Å/pix.
x 400 pix.
= 340. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.85 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.007
Minimum - Maximum-0.03027796 - 0.045309722
Average (Standard dev.)0.0000253368 (±0.0022296049)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 340.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_35174_msk_1.map
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Half map: #2

Fileemd_35174_half_map_1.map
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Half map: #1

Fileemd_35174_half_map_2.map
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Sample components

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Entire : Prochlorococcus phage P-SCSP1u

EntireName: Prochlorococcus phage P-SCSP1u (virus)
Components
  • Virus: Prochlorococcus phage P-SCSP1u (virus)
    • Protein or peptide: The capsid protein(gp 19) of P-SCSP1u

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Supramolecule #1: Prochlorococcus phage P-SCSP1u

SupramoleculeName: 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
Host (natural)Organism: Prochlorococcus (bacteria)

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Macromolecule #1: The capsid protein(gp 19) of P-SCSP1u

MacromoleculeName: The capsid protein(gp 19) of P-SCSP1u / type: protein_or_peptide / ID: 1 / Number of copies: 7 / Enantiomer: LEVO
Source (natural)Organism: Prochlorococcus phage P-SCSP1u (virus)
Molecular weightTheoretical: 35.160438 KDa
SequenceString: 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

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE / Chamber humidity: 100 %

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average exposure time: 4.5 sec. / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 81000
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.23 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 2.15) / Number images used: 732864
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 2.15)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 2.15)

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