9LBN | pdb_00009lbn

The composite cryo-EM structure of the head-to-tail connector and head-proximal tail components of bacteriophage phiXacJX1


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.60 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

Cryo-EM structures of a Xanthomonas phage: Insights into viral architecture and implications for the model phage HK97.

Guo, M.Wang, A.Zheng, Y.Liu, C.Shao, Q.Deng, Y.Li, L.Wang, Y.Wang, X.Shen, Y.Qian, J.Zhou, X.Fang, Q.

(2025) Structure 33: 1051-1062.e2

  • DOI: https://doi.org/10.1016/j.str.2025.03.013
  • Primary Citation of Related Structures:  
    9LBM, 9LBN

  • PubMed Abstract: 

    Xanthomonas bacteria are responsible for disease outbreaks in several hundred plant species, causing significant economic losses. Xanthomonas phages have emerged as a promising biocontrol strategy in managing various important plant diseases caused by Xanthomonas bacteria. However, structural information for Xanthomonas phages has remained limited so far. Here, we present high-resolution cryo-electron microscopy (cryo-EM) structures of the Xanthomonas citri phage ΦXacJX1 from siphoviruses. These structures include atomic models for the head, head-to-tail connector and head-proximal portion of the tail. ΦXacJX1's head and head-to-tail connector components show significant protein sequence and structural homology with those of the model siphophage HK97. However, the in-situ structures of head-to-tail connector of phage HK97 remain unavailable. The presented structures of phage ΦXacJX1 enhance our understanding of Xanthomonas phages and the mature virion of phage HK97. They provide a valuable framework for future structural and functional studies on both Xanthomonas phages and phage HK97.


  • Organizational Affiliation
    • School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, No. 66, Gongchang Road, Guangming District, Shenzhen, Guangdong 518107, China.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
portal protein gp1A [auth H],
G [auth h]
431Xanthomonas phage phiXacJX1Mutation(s): 0 
Entity Groups  
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
adaptor protein gp5B [auth I],
H [auth i]
111Xanthomonas phage phiXacJX1Mutation(s): 0 
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
stopper protein gp6C [auth J]124Xanthomonas phage phiXacJX1Mutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
terminator protein gp8D [auth K]118Xanthomonas phage phiXacJX1Mutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
tube protein gp9E [auth L],
F [auth M]
212Xanthomonas phage phiXacJX1Mutation(s): 0 
Entity Groups  
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION4.0
MODEL REFINEMENTPHENIX1.19.2-4158-000

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other government--

Revision History  (Full details and data files)

  • Version 1.0: 2025-05-07
    Type: Initial release
  • Version 1.1: 2025-06-18
    Changes: Data collection, Database references