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- PDB-9k09: Cyanophage A4 portal-tail complex -

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Basic information

Entry
Database: PDB / ID: 9k09
TitleCyanophage A4 portal-tail complex
Components
  • Portal protein
  • Tail fiber protein
  • Tail tubular protein A
  • Tail tubular protein B
KeywordsVIRAL PROTEIN / Cyanophage / Virus / Tail / Portal / Zozzle / Adaptor / Tail Fiber
Function / homologyPhage SU10 portal protein / Tail tubular protein A / Tail fiber protein / Portal protein / Tail tubular protein B
Function and homology information
Biological speciesAnabaena phage A-4L (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.6 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 15, 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

Downloads & links

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Assembly

Deposited unit
A: Tail fiber protein
B: Tail fiber protein
C: Tail fiber protein
D: Portal protein
E: Portal protein
F: Portal protein
G: Portal protein
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: Tail fiber protein
Q: Tail fiber protein
R: Tail fiber protein
U: Tail tubular protein B
V: Tail tubular protein B
W: Tail tubular protein B
X: Tail fiber protein
Y: Tail fiber protein
Z: Tail fiber protein
a: Tail fiber protein
b: Tail fiber protein
c: Tail fiber protein
d: Tail tubular protein A
e: Tail tubular protein A
f: Tail tubular protein A
g: Tail tubular protein A
h: Tail tubular protein A
i: Tail tubular protein A
j: Tail tubular protein A
k: Tail tubular protein A
l: Tail tubular protein A
m: Tail tubular protein A
n: Tail tubular protein A
o: Tail tubular protein A
p: Tail fiber protein
q: Tail fiber protein
r: Tail fiber protein
u: Tail tubular protein B
v: Tail tubular protein B
w: Tail tubular protein B
x: Tail fiber protein
y: Tail fiber protein
z: Tail fiber protein


Theoretical massNumber of molelcules
Total (without water)2,586,51948
Polymers2,586,51948
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
Tail fiber protein


Mass: 39873.277 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Source: (natural) Anabaena phage A-4L (virus) / References: UniProt: A0A059PY41
#2: Protein
Portal protein


Mass: 74284.602 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Anabaena phage A-4L (virus) / References: UniProt: A0A059PYA9
#3: Protein
Tail tubular protein B


Mass: 113330.102 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Anabaena phage A-4L (virus) / References: UniProt: A0A059PYE2
#4: Protein
Tail tubular protein A


Mass: 24783.678 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Anabaena phage A-4L (virus) / References: UniProt: A0A059PY25
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: 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: Tecnai F30 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F30
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: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 106052 / Symmetry type: POINT

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