9LC0 | pdb_00009lc0

tail complex of mature phage N4

  • Classification: VIRAL PROTEIN
  • Organism(s): Escherichia phage N4
  • Mutation(s): No 

  • Deposited: 2025-01-03 Released: 2025-04-16 
  • Deposition Author(s): Liu, H., Chen, W.
  • Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Asymmetric structure of podophage N4 from the Schitoviridae family reveals a type of tube-sheath short-tail architecture.

Zheng, J.Pang, H.Xiao, H.Zhou, J.Liu, Z.Chen, W.Liu, H.

(2025) Structure 33: 1250-1262.e2

  • DOI: https://doi.org/10.1016/j.str.2025.04.008
  • Primary Citation of Related Structures:  
    9LBZ, 9LC0, 9LC1, 9LD7

  • PubMed 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 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.


  • Organizational Affiliation
    • Institute of Interdisciplinary Studies, Key Laboratory for Matter Microstructure and Function of Hunan Province, Key Laboratory of Low-dimensional Quantum Structures and Quantum Control, School of Physics and Electronics, Hunan Normal University, Changsha 410082, China; The National & Local Joint Engineering Laboratory of Animal Peptide Drug Development, Peptide and Small Molecule Drug R&D Platform, Furong Laboratory, College of Life Sciences, Hunan Normal University, Changsha 410081, China.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
60 kDa protein556Escherichia phage N4Mutation(s): 0 
UniProt
Find proteins for A0MZE8 (Enterobacteria phage N4)
Explore A0MZE8 
Go to UniProtKB:  A0MZE8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0MZE8
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Gp64M,
N [auth R]
417Escherichia phage N4Mutation(s): 0 
UniProt
Find proteins for A0MZE6 (Enterobacteria phage N4)
Explore A0MZE6 
Go to UniProtKB:  A0MZE6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0MZE6
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Non-contractile tail sheathO [auth I],
P [auth N]
1,382Escherichia phage N4Mutation(s): 0 
UniProt
Find proteins for A0MZE7 (Enterobacteria phage N4)
Explore A0MZE7 
Go to UniProtKB:  A0MZE7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0MZE7
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
30 kDa proteinQ [auth J],
R [auth O],
S,
T [auth H]
236Escherichia phage N4Mutation(s): 0 
UniProt
Find proteins for A0MZE9 (Enterobacteria phage N4)
Explore A0MZE9 
Go to UniProtKB:  A0MZE9
Entity Groups  
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UniProt GroupA0MZE9
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  • Reference Sequence
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Gp54U [auth K],
V [auth P],
W [auth T],
X [auth U]
299Escherichia phage N4Mutation(s): 0 
UniProt
Find proteins for Q859Q3 (Enterobacteria phage N4)
Explore Q859Q3 
Go to UniProtKB:  Q859Q3
Entity Groups  
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UniProt GroupQ859Q3
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.19.2_4158

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China12034006
National Natural Science Foundation of China (NSFC)China32430020
National Natural Science Foundation of China (NSFC)China32071209
National Natural Science Foundation of China (NSFC)China32200994
National Natural Science Foundation of China (NSFC)China32401014
National Natural Science Foundation of China (NSFC)China32271329
National Natural Science Foundation of China (NSFC)China32071262

Revision History  (Full details and data files)

  • Version 1.0: 2025-04-16
    Type: Initial release
  • Version 1.1: 2025-10-29
    Changes: Data collection, Database references