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- EMDB-66307: Cryo-EM structure of the tail tip region of Parabacteroide phage ... -

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Basic information

Entry
Database: EMDB / ID: EMD-66307
TitleCryo-EM structure of the tail tip region of Parabacteroide phage PD491P1 (imposed with C6 symmetry)
Map data
Sample
  • Virus: Parabacteroides phage PD491P1 (virus)
    • Protein or peptide: tube protein
Keywordstail tube / Parabacteroides phage / VIRAL PROTEIN
Function / homology:
Function and homology information
Biological speciesParabacteroides phage PD491P1 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.1 Å
AuthorsCai C / Wang A / Shao Q
Funding support China, 3 items
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, 2025-
Header (metadata) releaseJun 24, 2026-
Map releaseJun 24, 2026-
UpdateJun 24, 2026-
Current statusJun 24, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_66307.png

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Map

FileDownload / File: emd_66307.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
1.29 Å/pix.
x 480 pix.
= 618.624 Å		1.29 Å/pix.
x 480 pix.
= 618.624 Å		1.29 Å/pix.
x 480 pix.
= 618.624 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.2888 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0068
Minimum - Maximum-0.021540446 - 0.03928863
Average (Standard dev.)0.000004727863 (±0.0016843696)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 618.624 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_66307_msk_1.map
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Half map: #2

Fileemd_66307_half_map_1.map
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Half map: #1

Fileemd_66307_half_map_2.map
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Sample components

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Entire : Parabacteroides phage PD491P1

EntireName: Parabacteroides phage PD491P1 (virus)
Components
  • Virus: Parabacteroides phage PD491P1 (virus)
    • Protein or peptide: tube protein

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Supramolecule #1: Parabacteroides phage PD491P1

SupramoleculeName: Parabacteroides phage PD491P1 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 2968687 / Sci species name: Parabacteroides phage PD491P1 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No

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Macromolecule #1: tube protein

MacromoleculeName: tube protein / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Parabacteroides phage PD491P1 (virus)
Molecular weightTheoretical: 23.218283 KDa
SequenceString: MITCKCPAAA SLPDIPAVKC AESFGQIQKV AFQRLTKDDG SKNSFTSEKA ITLLASWTPL LSAADSTKIV VSPYIQAPTN EAGAARTFG GGNETLGGVE EIIGREPNPF TGVMRKIPQS VIKAMKELQC ESWADNLGVY LFDENGSIEA IQDETVKTTY Y PIPIRSLF ...String:
MITCKCPAAA SLPDIPAVKC AESFGQIQKV AFQRLTKDDG SKNSFTSEKA ITLLASWTPL LSAADSTKIV VSPYIQAPTN EAGAARTFG GGNETLGGVE EIIGREPNPF TGVMRKIPQS VIKAMKELQC ESWADNLGVY LFDENGSIEA IQDETVKTTY Y PIPIRSLF IGDKTHGGLE APDSNAIQWA FLPNYSDNLT IIAPEFNPLT DLKVAVGG

UniProtKB: UNIPROTKB: A0AAE9VB33

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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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 24.9 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 75000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 20088
CTF correctionSoftware - Name: CTFFIND (ver. 4) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C6 (6 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0) / Number images used: 18749
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0)
FSC plot (resolution estimation)

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