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- PDB-9lbz: unique-vertex of mature phage N4 -

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Basic information

Entry
Database: PDB / ID: 9lbz
Titleunique-vertex of mature phage N4
Components
  • 32 kDa protein
  • Major capsid protein
  • Probable portal protein
KeywordsVIRAL PROTEIN / Complex
Function / homology
Function and homology information


symbiont genome ejection through host cell envelope, short tail mechanism / virion component / viral capsid
Similarity search - Function
Phage capsid protein / : / Phage SU10 portal protein / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
32 kDa protein / Probable portal protein / Major capsid protein
Similarity search - Component
Biological speciesEscherichia phage N4 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4 Å
AuthorsLiu, H. / Chen, W.
Funding support China, 7items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)12034006 China
National Natural Science Foundation of China (NSFC)32430020 China
National Natural Science Foundation of China (NSFC)32071209 China
National Natural Science Foundation of China (NSFC)32200994 China
National Natural Science Foundation of China (NSFC)32401014 China
National Natural Science Foundation of China (NSFC)32271329 China
National Natural Science Foundation of China (NSFC)32071262 China
CitationJournal: Structure / Year: 2025
Title: Asymmetric structure of podophage N4 from the Schitoviridae family reveals a type of tube-sheath short-tail architecture.
Authors: Jing Zheng / Hao Pang / Hao Xiao / Junquan Zhou / Zhonghua Liu / Wenyuan Chen / Hongrong Liu /
Abstract: The tails of the majority of reported podophages are typically composed of an adaptor, a nozzle, and a needle, and flanked by six or twelve fibers. However, the Schitoviridae family, as represented ...The tails of the majority of reported podophages are typically composed of an adaptor, a nozzle, and a needle, and flanked by six or twelve fibers. However, the Schitoviridae family, as represented by podophage N4, exhibits a different tail architecture that remains poorly understood. In this study, we employed cryoelectron microscopy (cryo-EM) to determine the atomic structures of mature and empty podophage N4 particles. The N4 tail, which is connected to the head by a portal and flanked by 12 fibers, comprises an adaptor, a 12-fold extended tail tube encircled by a 6-fold tail sheath, and a plug. The extended tail sheath is composed of two proteins, gp65 and gp64. Furthermore, we identified two distinct tail conformations in the mature podophage N4. Our structures provide insights into the mechanisms of ejection and early transcription of podophage N4, as well as for N4-like phages and CrAssphages.
History
DepositionJan 3, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Apr 16, 2025Provider: repository / Type: Initial release
Revision 1.0Apr 16, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Apr 16, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
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Revision 1.0Apr 16, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
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Revision 1.1Oct 29, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Probable portal protein
B: Probable portal protein
C: Probable portal protein
D: Probable portal protein
E: Probable portal protein
F: Probable portal protein
G: Probable portal protein
H: Probable portal protein
I: Probable portal protein
J: Probable portal protein
K: Probable portal protein
L: Probable portal protein
M: Major capsid protein
N: Major capsid protein
O: Major capsid protein
P: Major capsid protein
Q: Major capsid protein
R: Major capsid protein
S: Major capsid protein
T: Major capsid protein
U: Major capsid protein
V: Major capsid protein
W: Major capsid protein
X: Major capsid protein
Y: Major capsid protein
Z: Major capsid protein
a: Major capsid protein
b: Major capsid protein
c: Major capsid protein
d: Major capsid protein
e: Major capsid protein
f: Major capsid protein
g: Major capsid protein
h: Major capsid protein
i: Major capsid protein
j: Major capsid protein
k: Major capsid protein
l: Major capsid protein
m: Major capsid protein
n: Major capsid protein
o: Major capsid protein
p: Major capsid protein
q: 32 kDa protein
r: 32 kDa protein
s: 32 kDa protein
t: 32 kDa protein
u: 32 kDa protein
v: 32 kDa protein
w: 32 kDa protein
x: 32 kDa protein
y: 32 kDa protein
z: 32 kDa protein


Theoretical massNumber of molelcules
Total (without water)2,642,01452
Polymers2,642,01452
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
Probable portal protein / 94 kDa protein / Gene product 59 / gp59 / Head-to-tail connector


Mass: 85642.523 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Escherichia phage N4 (virus) / References: UniProt: A0MZE1
#2: Protein ...
Major capsid protein / Gene product 56 / gp56 / Major head protein


Mass: 44074.816 Da / Num. of mol.: 30 / Source method: isolated from a natural source / Source: (natural) Escherichia phage N4 (virus) / References: UniProt: Q859Q5
#3: Protein
32 kDa protein / gp17


Mass: 29205.900 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Source: (natural) Escherichia phage N4 (virus) / References: UniProt: A0MZA7
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: Escherichia phage N4 / Type: VIRUS / Entity ID: all / Source: NATURAL
Source (natural)Organism: Escherichia phage N4 (virus)
Details of virusEmpty: NO / Enveloped: NO / Isolate: SPECIES / Type: VIRION
Buffer solutionpH: 8
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: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 4000 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 32 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 15466 / Symmetry type: POINT

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