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- EMDB-65452: Cyanopodophage Pan3 tail complex -

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Basic information

Entry
Database: EMDB / ID: EMD-65452
TitleCyanopodophage Pan3 tail complex
Map data
Sample
  • Virus: Pseudanabaena phage Pan3 (virus)
    • Protein or peptide: Adaptor protein
    • Protein or peptide: Stabilization protein
    • Protein or peptide: Needle protein
    • Protein or peptide: Tail spike protein
    • Protein or peptide: Tail spike protein
    • Protein or peptide: Tail spike protein
KeywordsCyanophage / Virus / Tail / Adaptor / Nozzle / Needle / Tailspike / VIRAL PROTEIN
Function / homology: / : / : / :
Function and homology information
Biological speciesPseudanabaena phage Pan3 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsHou P / Zhou CZ / Jiang YL
Funding support China, 2 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32430001 China
National Natural Science Foundation of China (NSFC)92451302 China
CitationJournal: Structure / Year: 2026
Title: Cryo-EM structure of cyanopodophage Pan3 reveals a modular tail architecture for host recognition.
Authors: Pu Hou / Jie Zhu / Rong-Cheng Yu / Feng Yang / Kang Du / Jing Li / Wen-Wen Kong / Jie Wang / Yuxing Chen / Cong-Zhao Zhou / Yong-Liang Jiang /
Abstract: Cyanophages, which are bacteriophages that specifically infect host cyanobacteria, also utilize the tail to initiate host recognition and adsorption. Owing to the limited structural information on ...Cyanophages, which are bacteriophages that specifically infect host cyanobacteria, also utilize the tail to initiate host recognition and adsorption. Owing to the limited structural information on cyanophages, our understanding of the mechanism by which cyanophages specifically recognize their hosts remains largely unknown. Here, we determined the intact cryoelectron microscopy structure of a freshwater cyanopodophage Pan3, which consists of an icosahedral shell and a short tail comprising four modular components: the dodecameric adaptor, hexameric nozzle, trimeric needle, and six heterohexameric tailspikes. Notably, each tailspike features an SGNH esterase domain fused to a lectin domain, forming a continuous groove complementary to the host lipopolysaccharide. These findings provide insights into the receptor engagement in Podoviridae, and establish a structural framework for cyanophage and host interactions that may guide future antibacterial interventions against harmful blooms.
History
DepositionJul 21, 2025-
Header (metadata) releaseNov 26, 2025-
Map releaseNov 26, 2025-
UpdateFeb 25, 2026-
Current statusFeb 25, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_65452.png

Downloads & links

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Map

FileDownload / File: emd_65452.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 512 pix.
= 547.84 Å		1.07 Å/pix.
x 512 pix.
= 547.84 Å		1.07 Å/pix.
x 512 pix.
= 547.84 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.012
Minimum - Maximum-0.028816508 - 0.057978306
Average (Standard dev.)0.000021627515 (±0.002047069)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 547.84 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_65452_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_65452_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Pseudanabaena phage Pan3

EntireName: Pseudanabaena phage Pan3 (virus)
Components
  • Virus: Pseudanabaena phage Pan3 (virus)
    • Protein or peptide: Adaptor protein
    • Protein or peptide: Stabilization protein
    • Protein or peptide: Needle protein
    • Protein or peptide: Tail spike protein
    • Protein or peptide: Tail spike protein
    • Protein or peptide: Tail spike protein

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Supramolecule #1: Pseudanabaena phage Pan3

SupramoleculeName: Pseudanabaena phage Pan3 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 2981586 / Sci species name: Pseudanabaena phage Pan3 / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No

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Macromolecule #1: Adaptor protein

MacromoleculeName: Adaptor protein / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Pseudanabaena phage Pan3 (virus)
Molecular weightTheoretical: 19.930471 KDa
SequenceString:
MATCRDIVTR ALHMAAIVPL GKDPKAAEGQ LGLELLQGLY DGWFAGGMFG RLTDVYTDTA YTAKEGERVT VDGGTLTIPD TFEDTDTGL TRAPRELAAI VEINAGNITN RVWCGGEWQE CSGLTLNDEA PLSKRDAMGL SCLLALHMAE AFGTQIGPMT A RRGLQFQG SVSYKLGSTQ PDASGVYY

UniProtKB: UNIPROTKB: A0AA49CMD5

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Macromolecule #2: Stabilization protein

MacromoleculeName: Stabilization protein / type: protein_or_peptide / ID: 2 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Pseudanabaena phage Pan3 (virus)
Molecular weightTheoretical: 48.75391 KDa
SequenceString: MDLAYGTGAY ARTRGNLPEL PLVNLFVEAT RSDQRGVVLQ SRKGLVEDAE VGTGPIRGVF RKDGVLGGAE FVVSDDELYE DGVSLGTIN GTGPVSFAAI EDELLVCAGE SIWSYDGTTL DEVTFPDGAD VTKVAYSSGY FIALRAGTGQ WYFSALYDGT S WDGLDFAT ...String:
MDLAYGTGAY ARTRGNLPEL PLVNLFVEAT RSDQRGVVLQ SRKGLVEDAE VGTGPIRGVF RKDGVLGGAE FVVSDDELYE DGVSLGTIN GTGPVSFAAI EDELLVCAGE SIWSYDGTTL DEVTFPDGAD VTKVAYSSGY FIALRAGTGQ WYFSALYDGT S WDGLDFAT AESEPDALLD IVVLDGNPVF FGTQSVEFWS ATGDPDIPFA PIQNRTFEQG IFATGCAVAI DNSFFWVGAD KI VYRNDAV PVAVADDGIV ERATGSTDLR LFLLIDERHK FVCLRGDTFT MAFDITTNEW CEFQSYGRTN FRCGPDMGDD ETG IIWRFE GYSDNGGVLE RRFRAGATLP GPFRVNRLRL ICEVGTTPNL SGEYADPVIE MRASDDAGNT WGIWEGETLG AQGN YRQRV EWRALGLFDD PGMLFEHRMT APVSFRVTAV TVNGELGGRS R

UniProtKB: UNIPROTKB: A0AA49CMB9

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Macromolecule #3: Needle protein

MacromoleculeName: Needle protein / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Pseudanabaena phage Pan3 (virus)
Molecular weightTheoretical: 7.375228 KDa
SequenceString:
VSLRLDRLQR GVPIVDGQGR PNTQYQNLWQ RTVKALEADS AATADILQEL ADQLALIVAA QAAADAAQA

UniProtKB: UNIPROTKB: A0AA49CMD6

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Macromolecule #4: Tail spike protein

MacromoleculeName: Tail spike protein / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pseudanabaena phage Pan3 (virus)
Molecular weightTheoretical: 13.478897 KDa
SequenceString:
MAAQLFYLPF RPMLDANALA VPGAKLYFYA TGTTTKQPVY TSSALTTQLP NPVVANAAGK FPAIYLNDAL TYRCYIEDAD GNELADSDP YLASIADELT DELQDVVDAV EADRVAAANS ATAAATSAA

UniProtKB: UNIPROTKB: A0AA49HGR3

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Macromolecule #5: Tail spike protein

MacromoleculeName: Tail spike protein / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pseudanabaena phage Pan3 (virus)
Molecular weightTheoretical: 13.576935 KDa
SequenceString:
AAQLFYLPFR PMLDANALAV PGAKLYFYAT GTTTKQPVYT SSALTTQLPN PVVANAAGKF PAIYLNDALT YRCYIEDADG NELADSDPY LASIADELTD ELQDVVDAVE ADRVAAANSA TAAATSAAQT

UniProtKB: UNIPROTKB: A0AA49HGR3

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Macromolecule #6: Tail spike protein

MacromoleculeName: Tail spike protein / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pseudanabaena phage Pan3 (virus)
Molecular weightTheoretical: 13.276624 KDa
SequenceString:
AAQLFYLPFR PMLDANALAV PGAKLYFYAT GTTTKQPVYT SSALTTQLPN PVVANAAGKF PAIYLNDALT YRCYIEDADG NELADSDPY LASIADELTD ELQDVVDAVE ADRVAAANSA TAAATSA

UniProtKB: UNIPROTKB: A0AA49HGR3

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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: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 55.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING ONLY
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 119673
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: RANDOM ASSIGNMENT

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