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- PDB-9vzi: Cyanopodophage Pan3 Needle -

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Basic information

Entry
Database: PDB / ID: 9vzi
TitleCyanopodophage Pan3 Needle
ComponentsNeedle protein
KeywordsVIRUS / Cyanophage / Needle
Function / homologyIODIDE ION / :
Function and homology information
Biological speciesPseudanabaena phage Pan3 (virus)
MethodX-RAY DIFFRACTION / SAD / Resolution: 2.6 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 22, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Nov 26, 2025Provider: repository / Type: Initial release
Revision 1.1Jan 28, 2026Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Needle protein
C: Needle protein
D: Needle protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,81713
Polymers60,7573
Non-polymers1,06010
Water3,441191
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3900 Å2
ΔGint-23 kcal/mol
Surface area15780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.403, 71.403, 172.706
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number91
Space group name H-MP4122
Components on special symmetry positions
IDModelComponents
11C-361-

HOH

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Components

#1: Protein Needle protein


Mass: 20252.242 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudanabaena phage Pan3 (virus) / Gene: Pan3_08 / Production host: Escherichia coli (E. coli) / References: UniProt: A0AA49CMD6
#2: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: I
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 191 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.81 Å3/Da / Density % sol: 32.1 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 0.1 M HEPES pH 7.0 1.5 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54056 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Mar 10, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54056 Å / Relative weight: 1
ReflectionResolution: 2.6→13.02 Å / Num. obs: 14321 / % possible obs: 99.2 % / Redundancy: 16.5 % / CC1/2: 0.998 / Net I/σ(I): 26.7
Reflection shellResolution: 2.6→2.73 Å / Redundancy: 12 % / Mean I/σ(I) obs: 9.2 / Num. unique obs: 1877 / CC1/2: 0.978 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
REFMAC5refinement
CRANK2phasing
Cootmodel building
CrysalisProdata reduction
CrysalisProdata scaling
Aimlessdata scaling
CrysalisProdata collection
RefinementMethod to determine structure: SAD / Resolution: 2.6→13.02 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 18.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2199 656 4.58 %
Rwork0.1809 --
obs0.1828 14319 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.6→13.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2547 0 40 191 2778
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082607
X-RAY DIFFRACTIONf_angle_d0.9833555
X-RAY DIFFRACTIONf_dihedral_angle_d6.537390
X-RAY DIFFRACTIONf_chiral_restr0.058438
X-RAY DIFFRACTIONf_plane_restr0.007471
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.80.28351280.19032669X-RAY DIFFRACTION100
2.8-3.080.20961200.18372687X-RAY DIFFRACTION100
3.08-3.510.21241340.17162688X-RAY DIFFRACTION100
3.51-4.40.18741200.15952754X-RAY DIFFRACTION100

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