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- EMDB-65012: A block of bacteriophage SPO1 capsid -

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Basic information

Entry
Database: EMDB / ID: EMD-65012
TitleA block of bacteriophage SPO1 capsid
Map data
Sample
  • Virus: Bacillus phage SPO1 (virus)
KeywordsSPO1 / Phage / Capsid / VIRUS
Biological speciesBacillus phage SPO1 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsZhao X / Wang A / Wang Y / Kang Y / Shao Q / Li L / Zheng Y / Hu H / Li X / Fan H ...Zhao X / Wang A / Wang Y / Kang Y / Shao Q / Li L / Zheng Y / Hu H / Li X / Fan H / Cai C / Liu B / Fang Q
Funding support1 items
OrganizationGrant numberCountry
Other government
CitationJournal: Structure / Year: 2025
Title: Capsid structure of phage SPO1 reveals novel minor capsid proteins and insights into capsid stabilization.
Authors: Xinyue Zhao / Aohan Wang / Yueting Wang / Yue Kang / Qianqian Shao / Lin Li / Yaqi Zheng / Hongli Hu / Xiangyun Li / Hongling Fan / Can Cai / Bing Liu / Qianglin Fang /
Abstract: SPO1-related bacteriophages are promising candidates for phage therapy. We present the 3.0 Å cryo-electron microscopy (cryo-EM) structure of the SPO1 capsid with a triangulation number T = 16, ...SPO1-related bacteriophages are promising candidates for phage therapy. We present the 3.0 Å cryo-electron microscopy (cryo-EM) structure of the SPO1 capsid with a triangulation number T = 16, enabling the construction of an atomic model comprising the major capsid protein and three types of minor capsid proteins: gp29.2, gp2.7, and gp36.3. These minor capsid proteins adopt novel folds. They might stabilize the capsid and determine its curvature. Gp29.2 monomers contain a three-blade propeller fold and are located at the 3-fold and quasi-three-fold axes. Gp2.7 forms pentamers atop pentameric capsomers, while gp36.3 binds to the capsid's inner surface, forming star-shaped structures increasing connections between pentameric and hexameric capsomers. The surface exposed regions of gp29.2 and gp2.7 make SPO1 of interest as a nanocage for phage display. Our findings advance the understanding of capsid architecture, stabilization, and local curvature determination for SPO1-related bacteriophages.
History
DepositionJun 9, 2025-
Header (metadata) releaseAug 13, 2025-
Map releaseAug 13, 2025-
UpdateNov 26, 2025-
Current statusNov 26, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_65012.png

Downloads & links

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Map

FileDownload / File: emd_65012.map.gz / Format: CCP4 / Size: 307.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.37 Å/pix.
x 432 pix.
= 592.704 Å		1.37 Å/pix.
x 432 pix.
= 592.704 Å		1.37 Å/pix.
x 432 pix.
= 592.704 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.372 Å
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Histogram (log scale)
Contour LevelBy AUTHOR: 0.012
Minimum - Maximum-0.07176153 - 0.11999359
Average (Standard dev.)0.000108076536 (±0.0063608172)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions432432432
Spacing432432432
CellA=B=C: 592.704 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_65012_msk_1.map
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Half map: #2

Fileemd_65012_half_map_1.map
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Half map: #1

Fileemd_65012_half_map_2.map
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Sample components

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Entire : Bacillus phage SPO1

EntireName: Bacillus phage SPO1 (virus)
Components
  • Virus: Bacillus phage SPO1 (virus)

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Supramolecule #1: Bacillus phage SPO1

SupramoleculeName: Bacillus phage SPO1 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1-#4 / NCBI-ID: 2884427 / Sci species name: Bacillus phage SPO1 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No
Virus shellShell ID: 1 / Diameter: 1050.0 Å

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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: 8
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 26.3 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: CTFFIND (ver. 4) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 626340
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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