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- EMDB-66308: Cryo-EM structure of the tail tip region of Parabacteroide phage ... -

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Basic information

Entry
Database: EMDB / ID: EMD-66308
TitleCryo-EM structure of the tail tip region of Parabacteroide phage PD491P1 (imposed with C3 symmetry)
Map data
Sample
  • Virus: Parabacteroides phage PD491P1 (virus)
    • Protein or peptide: Tail protein
    • Protein or peptide: distal tail protein
Keywordshub / distal tail protein / Parabacteroides phage / VIRAL PROTEIN
Function / homology: / :
Function and homology information
Biological speciesParabacteroides phage PD491P1 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.5 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_66308.png

Downloads & links

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Map

FileDownload / File: emd_66308.map.gz / Format: CCP4 / Size: 421.9 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.)
1.29 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-0.015786845 - 0.029876266
Average (Standard dev.)-0.0000113630185 (±0.0015128274)
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_66308_msk_1.map
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Half map: #2

Fileemd_66308_half_map_1.map
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Half map: #1

Fileemd_66308_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: Tail protein
    • Protein or peptide: distal tail 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: Tail protein

MacromoleculeName: Tail protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Parabacteroides phage PD491P1 (virus)
Molecular weightTheoretical: 94.677875 KDa
SequenceString: MNSIYRFGFV NTFFVDGFAV GTDGTHTSPN YSYTKEYIPV SNIYPRKLFM SAAPENAGVW YDSNKNIISN FGSNPPAANV EFDIPNNAY YVRVNFSLSS RRAGSAWLRL GTMDADNYIA PYIVHPNYKD DLAKEYELET NQRFYRAKLS GKLSFIRDDY D YINNKPFD ...String:
MNSIYRFGFV NTFFVDGFAV GTDGTHTSPN YSYTKEYIPV SNIYPRKLFM SAAPENAGVW YDSNKNIISN FGSNPPAANV EFDIPNNAY YVRVNFSLSS RRAGSAWLRL GTMDADNYIA PYIVHPNYKD DLAKEYELET NQRFYRAKLS GKLSFIRDDY D YINNKPFD TTFLLLIEKS NDGGKTWTSY YSGQFMKTDC TFIDYDKKVT VQPDTIDEYN DVLAGLEKEY NLITLAPAIQ RI TINKRPL IQIYVPGDSI VSCFLGGANW EQDANATTDQ NALVQTYHFA LCNILKEIQI TSNGSPAVIS GLYTGRMATG ASA DAFEGK LYPELNVSYY IYISQQRIDG VPFGVALVEI RRQSDDVAMF RYQKVATSPF DTLEFDLTAV EGSGATGTMH ADMK SYNIY ARYLCDVDKI DDLNTYPLPA DDIVDNNRNY RRAIGYAIDV AFISNNFSDT PTEWGLADNG KYFAPPYSIY GQTFY PIAR STWRYASLWF GFYLMDWLLE EKARKAYTLR DAFPVASCIS VLLNQIAPGI THAATAEYSQ FLYSGNNPIS GLNFRL LVS QKTNIINGEY QQPAQKAPTT LQQFTNMLRD CFKCYWFIED GKFKIEHIQY FRNGGSYSGG AILSHDLTKE LNLRNGK PW AFNTSEYSFD KVDLPERYQF EWMDDVTAAF EGLPIQVISK YVTPGKVEEI NISNFTSDID MMLLNPGNMS SDGFALFA A VPPTSGSQWI LPFTRQTING VEYFLQNGYL AFINLQSPYW MYDLPARRVS INGSEVYAYG IERKKKQTFS FPANEDPNP MQLIKTYIGN GQVDKLSVNL HSRSIKATLK YDTE

UniProtKB: UNIPROTKB: A0AAE9VB06

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Macromolecule #2: distal tail protein

MacromoleculeName: distal tail protein / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Parabacteroides phage PD491P1 (virus)
Molecular weightTheoretical: 33.461461 KDa
SequenceString: MIQNNNFSVL PWYTSISEQN HRKSYAYGQI YPLFTPVNKF LPFQIMRNTR SNGITSVRIY HKDGTLFANV TQAAKDTGLQ VVRFASMGY DVIVYPGIIP MPITQLDGIY YATISDGVQT WYSEMYTIVQ DVSGYLKIEW YDIENAVFDA GTIVYQNPQF K NVLYLCTE ...String:
MIQNNNFSVL PWYTSISEQN HRKSYAYGQI YPLFTPVNKF LPFQIMRNTR SNGITSVRIY HKDGTLFANV TQAAKDTGLQ VVRFASMGY DVIVYPGIIP MPITQLDGIY YATISDGVQT WYSEMYTIVQ DVSGYLKIEW YDIENAVFDA GTIVYQNPQF K NVLYLCTE LGKPEYKFEE DGENRDGYFF PEKQISEKTY HCIFLAPEYL CDVMRFIRMS DYITVTDKYG HSYDCDTFLI TP KWQTQGD LASVEIEFET ETVVKKIGRG YIQQTGKGDY NSDFNNDFNN Q

UniProtKB: UNIPROTKB: A0AAE9VG28

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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 reconstructionResolution.type: BY AUTHOR / Resolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0) / Number images used: 18364
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0)
FSC plot (resolution estimation)

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