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- EMDB-66306: Cryo-EM Structure of Parabacteroide phage PD491P1 head-to-tail in... -

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Basic information

Entry
Database: EMDB / ID: EMD-66306
TitleCryo-EM Structure of Parabacteroide phage PD491P1 head-to-tail interface
Map data
Sample
  • Virus: Parabacteroides phage PD491P1 (virus)
    • Protein or peptide: tube protein
    • Protein or peptide: portal protein
    • Protein or peptide: adaptor protein
    • Protein or peptide: terminator protein
Keywordsneck / tail / Parabacteroide phage / VIRAL PROTEIN
Function / homology: / : / : / :
Function and homology information
Biological speciesParabacteroides phage PD491P1 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 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_66306.png

Downloads & links

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Map

FileDownload / File: emd_66306.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 360 pix.
= 386.64 Å		1.07 Å/pix.
x 360 pix.
= 386.64 Å		1.07 Å/pix.
x 360 pix.
= 386.64 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.074 Å
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Histogram (log scale)
Contour LevelBy AUTHOR: 0.0055
Minimum - Maximum-0.017144805 - 0.034100737
Average (Standard dev.)-0.0000132544765 (±0.0019133685)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 386.64 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_66306_msk_1.map
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Half map: #2

Fileemd_66306_half_map_1.map
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Half map: #1

Fileemd_66306_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
    • Protein or peptide: portal protein
    • Protein or peptide: adaptor protein
    • Protein or peptide: terminator protein

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Supramolecule #1: Parabacteroides phage PD491P1

SupramoleculeName: Parabacteroides phage PD491P1 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #2-#4, #1 / 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: terminator protein

MacromoleculeName: terminator protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Parabacteroides phage PD491P1 (virus)
Molecular weightTheoretical: 21.744586 KDa
SequenceString:
MDRVPIIKNP ELFDRVIANI QKGLADGLPW LNYSFGRSER LVKSIQGKRY YTPNIYVGGN EYMLIAPDSN IGNFSFFVLD DPQQIDWFP GEQNKYTTPF SVIFWFDMRT ITNDPNNRNT EAVKQQIMRV LNGGIWLRSG SMTINRVYAK AENIFAGFTL D EIDNQFLM HPFAGFRFAG ELGIDETCLT D

UniProtKB: UNIPROTKB: A0AAE9VCM6

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Macromolecule #2: tube protein

MacromoleculeName: tube protein / type: protein_or_peptide / ID: 2 / Number of copies: 2 / 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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Macromolecule #3: portal protein

MacromoleculeName: portal protein / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Parabacteroides phage PD491P1 (virus)
Molecular weightTheoretical: 67.373312 KDa
SequenceString: MGLDISEIKK RITEPKKRNT INRAIYHQQR INFHARTRIT SFDICQPITD FMAFVSNLLP HDKFKMFKTL FRYPVKTNEV TGVCFDKLS RIFDGRNPAF NYQFQNPEQR DDWEYYRQDV LHEPEIWSTK GWEFFQTEIN SVLIVDMPSE QNPGDKYPQP Y FYWLPIAS ...String:
MGLDISEIKK RITEPKKRNT INRAIYHQQR INFHARTRIT SFDICQPITD FMAFVSNLLP HDKFKMFKTL FRYPVKTNEV TGVCFDKLS RIFDGRNPAF NYQFQNPEQR DDWEYYRQDV LHEPEIWSTK GWEFFQTEIN SVLIVDMPSE QNPGDKYPQP Y FYWLPIAS VIDYRANPTT GVMDYIIFRQ DGERIAVIDD ERYRVFREDK NHNIGELLVD NPHDVGYCPA RFFWNEPLSL SE PDVKQSP LTKQLEALDW FLFYHISKRH LDLYGAYPIY SGYEQSCDFS NGENGDYCDG GFLKDKQGFY RLDAAGLLMR CPK CGDSRI NGVGSFVEIP IPDGDKQPDL RNPVQMLTVD RGSLDYNVEE ENRLKNDIIT SVVGTNEEIT TRDALNEQQI QANF ESQST VLNRVKKGFE AAQQFVDETV CRLRYGGLFV SAKVNYGTEF YLSNATELRE RYKVAKESGA SEAELDALQN QIIET EYRN NPTQLQRMLT LAELEPYRHL TRNEVLDLYD KQIISENDMR IKLNFANFVR RFEREYLNVL EFGYNMPFNS KINFIT SKF NDYASESKRG QN

UniProtKB: UNIPROTKB: A0A9Y1HT91

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Macromolecule #4: adaptor protein

MacromoleculeName: adaptor protein / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Parabacteroides phage PD491P1 (virus)
Molecular weightTheoretical: 49.814086 KDa
SequenceString: MYRIKEIQDK LLHVVGWEQS YNPAEAIAER LTETESGLYF QGAHPLVTLD NMAAIVPDNW GYQYPVWNDT KEWKAGTVVQ YANDAAGKP LYWVALVDNV AEVPAEGSTY WEKYNILSDY LERLTRNGIS TAVQTFTQIK GLDKETKNLL ERRTFFDGAG R IRATQPNN ...String:
MYRIKEIQDK LLHVVGWEQS YNPAEAIAER LTETESGLYF QGAHPLVTLD NMAAIVPDNW GYQYPVWNDT KEWKAGTVVQ YANDAAGKP LYWVALVDNV AEVPAEGSTY WEKYNILSDY LERLTRNGIS TAVQTFTQIK GLDKETKNLL ERRTFFDGAG R IRATQPNN HKLVGFEIIP VRAMGVTAQI HRVGLQMTGG TGIVKLYLFH SSQIDPVKTF DLNFTLTNGG FQWFTLEDCF LP YISDANN AGGAWFLCYN QDDLPAGMQA INVSKDWSRE PCGTCTGYGN IEAWRQLTKY LQISPFMYNA PETFAEYPEL WDI AYTMYT NTLNYGLNCE ITVGCDLTDF IVEQRAIFQT VIQRQVAAIA LRTLAMNPNV RVNRNQSNAS KMEILYELDG NVEG RPGGL GYDLKKAFEA LRLDTQGIDR ICLSCNNRGV KYRTT

UniProtKB: UNIPROTKB: A0AAF0AFG4

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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
GridModel: Quantifoil R2/1 / Material: COPPER / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE
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: 85662
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C6 (6 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 21657
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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