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- PDB-9k3a: Cyanophage A4 pre-ejectosome with C1 symmetry -

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Basic information

Entry
Database: PDB / ID: 9k3a
TitleCyanophage A4 pre-ejectosome with C1 symmetry
Components(Tail protein) x 2
KeywordsVIRAL PROTEIN / Cyanophage / Virus / Capsid
Function / homologyTail protein / Tail protein
Function and homology information
Biological speciesAnabaena phage A-4L (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsHou, P. / Li, Q. / Zhou, C.Z.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)U19A2020 China
CitationJournal: Proc Natl Acad Sci U S A / Year: 2025
Title: Cryo-EM structure of cyanopodophage A4 reveals a pentameric pre-ejectosome in the double-stabilized capsid.
Authors: Pu Hou / Rui-Qian Zhou / Yong-Liang Jiang / Rong-Cheng Yu / Kang Du / Nanqin Gan / Fei Ke / Qi-Ya Zhang / Qiong Li / Cong-Zhao Zhou /
Abstract: Upon infection, the podophages usually eject a couple of proteins from the capsid to form a transmembrane ejectosome on the host cell membrane that facilitates the ejection of viral genome. However, ...Upon infection, the podophages usually eject a couple of proteins from the capsid to form a transmembrane ejectosome on the host cell membrane that facilitates the ejection of viral genome. However, it remains unclear how these proteins of pre-ejectosome are finely assembled at the center of highly packaged genome. Here, we report the intact structure of cyanopodophage A4, which consists of a capsid stabilized by two types of cement proteins and a short tail attached with six tail fibers. Notably, we find a pentameric pre-ejectosome at the core of capsid, which is composed of four ejection proteins wrapped into a coaxial cylinder of triple layers. Moreover, a segment of genomic DNA runs along the positively charged circular cleft formed by two ejection proteins. Based on the mortise-and-tenon architecture of pre-ejectosome in combination with previous studies, we propose a putative DNA packaging process and ejection mechanism for podophages. These findings largely enrich our knowledge on the assembly mechanism of podophages, which might facilitate the application of A4 as a chassis cyanophage in synthetic biology.
History
DepositionOct 18, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 9, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tail protein
B: Tail protein


Theoretical massNumber of molelcules
Total (without water)315,7102
Polymers315,7102
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Tail protein / gp26


Mass: 125851.086 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Anabaena phage A-4L (virus) / References: UniProt: A0A059PYE1
#2: Protein Tail protein


Mass: 189859.203 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Anabaena phage A-4L (virus) / References: UniProt: A0A059PY24
Has protein modificationY

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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: Anabaena phage A-4L / Type: VIRUS / Entity ID: all / Source: NATURAL
Source (natural)Organism: Anabaena phage A-4L (virus)
Details of virusEmpty: NO / Enveloped: NO / Isolate: SPECIES / Type: VIRION
Natural hostOrganism: Nostoc sp. PCC 7120 = FACHB-418
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 softwareName: RELION / Version: 3.1 / Category: 3D reconstruction
CTF correctionType: PHASE FLIPPING ONLY
3D reconstructionResolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 535710 / Symmetry type: POINT
RefinementHighest resolution: 3.6 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00916444
ELECTRON MICROSCOPYf_angle_d0.87122271
ELECTRON MICROSCOPYf_dihedral_angle_d5.7052221
ELECTRON MICROSCOPYf_chiral_restr0.0412514
ELECTRON MICROSCOPYf_plane_restr0.0082914

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