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- EMDB-65449: Cyanopodophage Pan3 capsid -

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Basic information

Entry
Database: EMDB / ID: EMD-65449
TitleCyanopodophage Pan3 capsid
Map data
Sample
  • Virus: Pseudanabaena phage Pan3 (virus)
    • Protein or peptide: Major capsid protein
KeywordsCyanophage / Virus / Capsid / Major capsid protein
Function / homology:
Function and homology information
Biological speciesPseudanabaena phage Pan3 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 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: 2025
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-
UpdateJan 28, 2026-
Current statusJan 28, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_65449.png

Downloads & links

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Map

FileDownload / File: emd_65449.map.gz / Format: CCP4 / Size: 1.3 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 700 pix.
= 749. Å		1.07 Å/pix.
x 700 pix.
= 749. Å		1.07 Å/pix.
x 700 pix.
= 749. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.03
Minimum - Maximum-0.09058769 - 0.14414333
Average (Standard dev.)0.0012205818 (±0.0074485485)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions700700700
Spacing700700700
CellA=B=C: 749.00006 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_65449_half_map_1.map
Projections & Slices
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Half map: #1

Fileemd_65449_half_map_2.map
Projections & Slices
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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: Major capsid 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: Major capsid protein

MacromoleculeName: Major capsid protein / type: protein_or_peptide / ID: 1 / Number of copies: 7 / Enantiomer: LEVO
Source (natural)Organism: Pseudanabaena phage Pan3 (virus)
Molecular weightTheoretical: 39.866551 KDa
SequenceString: MADTTPATGL VVQQWEDKFF QEYLHDGGFK ALMGTDENAV IQVKEDLSKK AGDSITIALV NRLNNAAVTG ASTLEGNEED MTSRSLRIY VDKRRNAVRI AEISEQRSAI SLRNAARATL LDWAMEDTRD LIIEALGSLN GTRFVDRTAA IADAWLVDNL D RVYFGAGV ...String:
MADTTPATGL VVQQWEDKFF QEYLHDGGFK ALMGTDENAV IQVKEDLSKK AGDSITIALV NRLNNAAVTG ASTLEGNEED MTSRSLRIY VDKRRNAVRI AEISEQRSAI SLRNAARATL LDWAMEDTRD LIIEALGSLN GTRFVDRTAA IADAWLVDNL D RVYFGAGV GSGTDLSADL AQLDTSADLF NVAALDGMIL KAKTCNPKIR PMRDPGNGKR YYVAFANPHA FKNLRDSMDN EY LSNTVVQ MQASKLFEGG DLMWNGVIVK ETDNIPIYEN LGAGGTAEVT PVYLCGAQAL AVAYAKRWKT VTEEFDYGDK YGV AVDGIY GVRKIIFGSG SGDTDDLKDH GVVTGFFATT GAATVAAAAA AEN

UniProtKB: UNIPROTKB: A0AA49CM87

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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: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 191214
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: RANDOM ASSIGNMENT

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