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- PDB-9wwc: Cryo-EM structure of the tail tip region of Parabacteroide phage ... -

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Basic information

Entry
Database: PDB / ID: 9wwc
TitleCryo-EM structure of the tail tip region of Parabacteroide phage PD491P1 (imposed with C3 symmetry)
Components
  • Tail protein
  • distal tail protein
KeywordsVIRAL PROTEIN / hub / distal tail protein / Parabacteroides phage
Function / homology: / :
Function and homology information
Biological speciesParabacteroides phage PD491P1 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.5 Å
AuthorsCai, C. / Wang, A. / Shao, Q.
Funding support China, 3items
OrganizationGrant numberCountry
Other governmentD2301008
Other governmentJCYJ20240813180500001
National Natural Science Foundation of China (NSFC)32371285 China
CitationJournal: Structure / Year: 2026
Title: Cryo-EM structures of prevalent gut phage PD491P1 uncover extensive disulfide stabilization and distinct structural adaptations.
Authors: Can Cai / Aohan Wang / Qianqian Shao / Jieqiong Zhang / Yueting Wang / Hongli Hu / Ke Yuan / Lin Li / Xiaofang Wang / Qianglin Fang / Yingfei Ma /
Abstract: Bacteriophages play crucial roles in modulating the human gut microbiome, yet structural characterization of prevalent gut phages remains limited. Here, we present high-resolution cryo-EM structures ...Bacteriophages play crucial roles in modulating the human gut microbiome, yet structural characterization of prevalent gut phages remains limited. Here, we present high-resolution cryo-EM structures of Parabacteroides phage PD491P1, which is one of the most abundant bacteriophages in the human gut. The structures reveal its mature virion organization, including the capsid, head-to-tail interface, and tail tip regions. Strikingly, PD491P1 exhibits an exceptionally extensive disulfide bond network that covalently stabilizes nearly the entire virion. Unique structural features include an elaborate portal-adaptor-terminator interface and distinctive, upward-pointing and flexible tail fibers with multiple putative host recognition domains. These structural adaptations may enable phage PD491P1 to achieve survival and robust infection in the challenging gut environment. These findings expand our understanding of gut phage structural diversity, reveal mechanistic insights into phage stability and infection, and provide a foundation for future development of phage-based microbiome therapeutics.
History
DepositionSep 23, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jun 24, 2026Provider: repository / Type: Initial release
Revision 1.0Jun 24, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jun 24, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jun 24, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 24, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 24, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jun 24, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Jun 24, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Tail protein
S: distal tail protein
A: distal tail protein


Theoretical massNumber of molelcules
Total (without water)161,6013
Polymers161,6013
Non-polymers00
Water00
1
B: Tail protein
S: distal tail protein
A: distal tail protein

B: Tail protein
S: distal tail protein
A: distal tail protein

B: Tail protein
S: distal tail protein
A: distal tail protein


Theoretical massNumber of molelcules
Total (without water)484,8029
Polymers484,8029
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation2

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Components

#1: Protein Tail protein


Mass: 94677.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Parabacteroides phage PD491P1 (virus) / References: UniProt: A0AAE9VB06
#2: Protein distal tail protein


Mass: 33461.461 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Parabacteroides phage PD491P1 (virus) / References: UniProt: A0AAE9VG28
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: Parabacteroides phage PD491P1 / Type: VIRUS / Entity ID: all / Source: NATURAL
Source (natural)Organism: Parabacteroides phage PD491P1 (virus)
Details of virusEmpty: NO / Enveloped: NO / Isolate: STRAIN / Type: VIRION
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen 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 magnification: 75000 X / Nominal defocus max: 2400 nm / Nominal defocus min: 1200 nm
Specimen holderSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 24.9 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1RELION4particle selection
2PHENIX1.19.2_4158:model refinement
5CTFFIND4CTF correction
11RELION4final Euler assignment
13RELION43D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 20088
3D reconstructionResolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 18364 / Symmetry type: POINT

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