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- EMDB-65011: The composite cryo-EM structure of bacteriophage SPO1 capsid -

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Basic information

Entry
Database: EMDB / ID: EMD-65011
TitleThe composite cryo-EM structure of bacteriophage SPO1 capsid
Map data
Sample
  • Virus: Bacillus phage SPO1 (virus)
    • Protein or peptide: Gp6.1
    • Protein or peptide: Gp29.2
    • Protein or peptide: Gp2.7
    • Protein or peptide: Gp36.3
KeywordsSPO1 / Phage / Capsid / VIRUS
Function / homologyProtein of unknown function DUF5309 / SU10 major capsid protein / membrane / Gp36.3 / Gp29.2 / Gp2.7 / Gp6.1
Function and homology information
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 27, 2025-
Map releaseAug 27, 2025-
UpdateNov 26, 2025-
Current statusNov 26, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_65011.png

Downloads & links

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Map

FileDownload / File: emd_65011.map.gz / Format: CCP4 / Size: 3.8 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.37 Å/pix.
x 1008 pix.
= 1382.976 Å		1.37 Å/pix.
x 1008 pix.
= 1382.976 Å		1.37 Å/pix.
x 1008 pix.
= 1382.976 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.372 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.011
Minimum - Maximum-0.062363453 - 0.11162624
Average (Standard dev.)0.0000962817 (±0.0035669745)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-504-504-504
Dimensions100810081008
Spacing100810081008
CellA=B=C: 1382.976 Å
α=β=γ: 90.0 °

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Supplemental data

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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)
    • Protein or peptide: Gp6.1
    • Protein or peptide: Gp29.2
    • Protein or peptide: Gp2.7
    • Protein or peptide: Gp36.3

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Supramolecule #1: Bacillus phage SPO1

SupramoleculeName: Bacillus phage SPO1 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / 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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Macromolecule #1: Gp6.1

MacromoleculeName: Gp6.1 / type: protein_or_peptide / ID: 1 / Number of copies: 16 / Enantiomer: LEVO
Source (natural)Organism: Bacillus phage SPO1 (virus)
Molecular weightTheoretical: 51.445043 KDa
SequenceString: MNFGNGVNGF GNGSQADVDA LNKALEAGHT VNPLDLEGGG AFRVESLERS LHNLSFTDQH IKFWKKIPKQ KAYSTVEQYG QLLDYGRSQ GAFVGEGVLP DTNDSTYARK AAFVKFLGTT REVTHPMTLV NSAFGNVIAR QNKDGILWML KQIEQALFWG D SKLAPGGQ ...String:
MNFGNGVNGF GNGSQADVDA LNKALEAGHT VNPLDLEGGG AFRVESLERS LHNLSFTDQH IKFWKKIPKQ KAYSTVEQYG QLLDYGRSQ GAFVGEGVLP DTNDSTYARK AAFVKFLGTT REVTHPMTLV NSAFGNVIAR QNKDGILWML KQIEQALFWG D SKLAPGGQ EGLQFDGINK MIDPENTIDL KGNYLEEKHI NWGSQLILQN YGTPTDLMLP FEVMGQFSQE FFPKERVIMP TN DGYQAGV VVNKFMTHGG EVDFTPNLFL NKTTPLNMNA SSQKAPAPGT LAAEIGTAND AEFGKQTGGG AGVYKYAVTF NNS HGESVP SNIVDVTIAN EDVAKGVKLT ITNPVSTAFP VEYIKVYRSE KDGQRLYEVA KFAVTTDNSG GVTEHTDKCE ILAN TYTAF MGEMSEEVIA FKQLTPMMKM DLATLGPVIR WMILMYGVPV MYAPKKFMKY TNIKADVPGY IGN

UniProtKB: Gp6.1

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Macromolecule #2: Gp29.2

MacromoleculeName: Gp29.2 / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Bacillus phage SPO1 (virus)
Molecular weightTheoretical: 19.837922 KDa
SequenceString:
MLFKYIHDVN AKVEEGRRYL SDVVRVALDK EETTDPDTQE VTSTSYRVTA YPVVQVGEEE VPYIPVHPKT AEPGQKVTVP TYDVPEKLP VLVRGRNPEA TGDYDDHIWV TEEVEVRPLV DEVFKEDEFE KARLYYENVA AQLAEGDDIR HYYRKDLDRE A GHYSVSRY PSF

UniProtKB: Gp29.2

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Macromolecule #3: Gp2.7

MacromoleculeName: Gp2.7 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacillus phage SPO1 (virus)
Molecular weightTheoretical: 6.380301 KDa
SequenceString:
MTKLRLITGT VYTEMSAAEV RSYLQRGSKA GTINGYEDEA KTVPILISVE SIEYIYL

UniProtKB: Gp2.7

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Macromolecule #4: Gp36.3

MacromoleculeName: Gp36.3 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacillus phage SPO1 (virus)
Molecular weightTheoretical: 10.812946 KDa
SequenceString:
MNHNIQDLQM HANEVCRQIG AKAVQDYLKK VDPDMVLAYS DERGYFIFDP NEEPPTGSGN GETASQVELY IDLTKPLEGA DFRRYESPN PSTITLP

UniProtKB: Gp36.3

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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

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