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- PDB-9vyf: Cyanopodophage Pan3 portal complex -

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Basic information

Entry
Database: PDB / ID: 9vyf
TitleCyanopodophage Pan3 portal complex
ComponentsPortal protein
KeywordsVIRAL PROTEIN / Cyanophage / Virus / Portal
Function / homology:
Function and homology information
Biological speciesPseudanabaena phage Pan3 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsHou, P. / Zhou, C.Z. / Jiang, Y.L.
Funding support China, 2items
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, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Nov 26, 2025Provider: repository / Type: Initial release
Revision 1.0Nov 26, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
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Revision 1.1Jan 28, 2026Group: Data collection / Database references / Category: citation / citation_author / em_admin
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: Portal protein
I: Portal protein
J: Portal protein
K: Portal protein
L: Portal protein
M: Portal protein
N: Portal protein
O: Portal protein
P: Portal protein
Q: Portal protein
R: Portal protein
S: Portal protein


Theoretical massNumber of molelcules
Total (without water)831,85412
Polymers831,85412
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Portal protein


Mass: 69321.203 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Pseudanabaena phage Pan3 (virus) / References: UniProt: A0AA49HFY0
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Pseudanabaena phage Pan3 / Type: VIRUS / Entity ID: all / Source: NATURAL
Source (natural)Organism: Pseudanabaena phage Pan3 (virus)
Details of virusEmpty: NO / Enveloped: NO / Isolate: SPECIES / Type: VIRION
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1500 nm
Image recordingElectron dose: 55 e/Å2 / Film or detector model: GATAN K2 QUANTUM (4k x 4k)

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Processing

EM software
IDNameCategory
1RELIONparticle selection
13RELION3D reconstruction
CTF correctionType: PHASE FLIPPING ONLY
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 120202 / Symmetry type: POINT
RefinementHighest resolution: 3.3 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00252554
ELECTRON MICROSCOPYf_angle_d0.46971045
ELECTRON MICROSCOPYf_dihedral_angle_d3.3047221
ELECTRON MICROSCOPYf_chiral_restr0.0397704
ELECTRON MICROSCOPYf_plane_restr0.0049460

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