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 9LBM | pdb_00009lbm

Cryo-EM structure of bacteriophage phiXacJX1 capsid


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 9LBM

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 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.

Macromolecule Content 

  • Total Structure Weight: 292.95 kDa 
  • Atom Count: 15,015 
  • Modeled Residue Count: 2,002 
  • Deposited Residue Count: 2,758 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
major capsid protein gp3394Xanthomonas phage phiXacJX1Mutation(s): 0 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 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
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