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- PDB-9vyf: Cyanopodophage Pan3 portal complex -

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ID or keywords:

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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: To Be Published
Title: Cryo-EM structure of cyanopodophage Pan3 reveals a new host recognition mode
Authors: Hou, P. / Zhou, C.Z. / Jiang, Y.L.
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
Revision 1.0Nov 26, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Nov 26, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Nov 26, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Nov 26, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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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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