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- PDB-9k2v: Cyanophage A4 pre-ejectosome -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 9k2v
TitleCyanophage A4 pre-ejectosome
Components
  • Internal protein
  • Internal virion protein
  • Portal protein
KeywordsVIRAL PROTEIN / Cyanophage / Virus / Ejectosome
Function / homology
Function and homology information


metalloendopeptidase activity / killing of cells of another organism / defense response to bacterium
Similarity search - Function
: / Phage SU10 portal protein / : / Peptidase M23 / Peptidase family M23 / Duplicated hybrid motif
Similarity search - Domain/homology
Internal virion protein / Internal protein / Portal protein
Similarity search - Component
Biological speciesAnabaena phage A-4L (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 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
Revision 1.0Apr 9, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Apr 9, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 9, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 9, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Apr 9, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Jul 2, 2025Group: Data collection / Category: em_admin / em_software / Item: _em_admin.last_update / _em_software.name
Revision 1.1Jul 2, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Data processing / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / em_software / Data content type: EM metadata / EM metadata / Item: _em_admin.last_update / _em_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
K: Portal protein
M: Portal protein
O: Portal protein
G: Portal protein
I: Portal protein
F: Portal protein
H: Portal protein
J: Portal protein
L: Portal protein
N: Portal protein
V: Internal virion protein
W: Internal virion protein
X: Internal virion protein
Y: Internal virion protein
Z: Internal virion protein
v: Internal virion protein
w: Internal virion protein
x: Internal virion protein
y: Internal virion protein
z: Internal virion protein
E: Internal protein
d: Internal protein
A: Internal protein
e: Internal protein
B: Internal protein
a: Internal protein
C: Internal protein
b: Internal protein
D: Internal protein
c: Internal protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,315,25835
Polymers2,314,93130
Non-polymers3275
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
Portal protein


Mass: 74284.602 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Source: (natural) Anabaena phage A-4L (virus) / References: UniProt: A0A059PYA9
#2: Protein
Internal virion protein / gp29A/B


Mass: 40871.699 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Source: (natural) Anabaena phage A-4L (virus) / References: UniProt: A0A059PY42
#3: Protein
Internal protein / gp28A


Mass: 116336.844 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Source: (natural) Anabaena phage A-4L (virus) / References: UniProt: A0A059PY91
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
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: #1-#3 / 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: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING ONLY
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 107142 / Symmetry type: POINT
RefinementHighest resolution: 3.4 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00264235
ELECTRON MICROSCOPYf_angle_d0.45186735
ELECTRON MICROSCOPYf_dihedral_angle_d3.2328970
ELECTRON MICROSCOPYf_chiral_restr0.0359555
ELECTRON MICROSCOPYf_plane_restr0.00411685

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