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- PDB-9vel: The composite cryo-EM structure of bacteriophage SPO1 capsid -

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Basic information

Entry
Database: PDB / ID: 9vel
TitleThe composite cryo-EM structure of bacteriophage SPO1 capsid
Components
  • Gp2.7
  • Gp29.2
  • Gp36.3
  • Gp6.1
KeywordsVIRUS / SPO1 / Phage / Capsid
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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 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 support1items
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, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Aug 27, 2025Provider: repository / Type: Initial release
Revision 1.0Aug 27, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Aug 27, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Aug 27, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Sep 10, 2025Group: Data collection / Database references / Category: citation / em_admin
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Gp6.1
F: Gp6.1
G: Gp6.1
D: Gp6.1
I: Gp6.1
J: Gp6.1
O: Gp6.1
N: Gp6.1
M: Gp6.1
H: Gp6.1
K: Gp6.1
L: Gp6.1
B: Gp6.1
r: Gp29.2
q: Gp29.2
s: Gp29.2
E: Gp6.1
P: Gp6.1
A: Gp6.1
t: Gp2.7
v: Gp29.2
w: Gp36.3


Theoretical massNumber of molelcules
Total (without water)919,66622
Polymers919,66622
Non-polymers00
Water00
1
C: Gp6.1
F: Gp6.1
G: Gp6.1
D: Gp6.1
I: Gp6.1
J: Gp6.1
O: Gp6.1
N: Gp6.1
M: Gp6.1
H: Gp6.1
K: Gp6.1
L: Gp6.1
B: Gp6.1
r: Gp29.2
q: Gp29.2
s: Gp29.2
E: Gp6.1
P: Gp6.1
A: Gp6.1
t: Gp2.7
v: Gp29.2
w: Gp36.3
x 60


Theoretical massNumber of molelcules
Total (without water)55,179,9371320
Polymers55,179,9371320
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
2


  • Idetical with deposited unit
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Gp6.1
F: Gp6.1
G: Gp6.1
D: Gp6.1
I: Gp6.1
J: Gp6.1
O: Gp6.1
N: Gp6.1
M: Gp6.1
H: Gp6.1
K: Gp6.1
L: Gp6.1
B: Gp6.1
r: Gp29.2
q: Gp29.2
s: Gp29.2
E: Gp6.1
P: Gp6.1
A: Gp6.1
t: Gp2.7
v: Gp29.2
w: Gp36.3
x 5


  • icosahedral pentamer
  • 4.6 MDa, 110 polymers
Theoretical massNumber of molelcules
Total (without water)4,598,328110
Polymers4,598,328110
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
C: Gp6.1
F: Gp6.1
G: Gp6.1
D: Gp6.1
I: Gp6.1
J: Gp6.1
O: Gp6.1
N: Gp6.1
M: Gp6.1
H: Gp6.1
K: Gp6.1
L: Gp6.1
B: Gp6.1
r: Gp29.2
q: Gp29.2
s: Gp29.2
E: Gp6.1
P: Gp6.1
A: Gp6.1
t: Gp2.7
v: Gp29.2
w: Gp36.3
x 6


  • icosahedral 23 hexamer
  • 5.52 MDa, 132 polymers
Theoretical massNumber of molelcules
Total (without water)5,517,994132
Polymers5,517,994132
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
5


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))

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Components

#1: Protein
Gp6.1


Mass: 51445.043 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Source: (natural) Bacillus phage SPO1 (virus) / References: UniProt: B6V2N7
#2: Protein
Gp29.2


Mass: 19837.922 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Bacillus phage SPO1 (virus) / References: UniProt: B6V2J1
#3: Protein Gp2.7


Mass: 6380.301 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus phage SPO1 (virus) / References: UniProt: B6V2M7
#4: Protein Gp36.3


Mass: 10812.946 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus phage SPO1 (virus) / References: UniProt: B6V2H5
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Bacillus phage SPO1 / Type: VIRUS / Entity ID: all / Source: NATURAL
Source (natural)Organism: Bacillus phage SPO1 (virus)
Details of virusEmpty: NO / Enveloped: NO / Isolate: STRAIN / Type: VIRION
Virus shellDiameter: 1050 nm
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 26.3 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1RELION4particle selection
4CTFFIND4CTF correction
10RELION4initial Euler assignment
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 626340 / Symmetry type: POINT

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