9IK0 | pdb_00009ik0

Crystal structure of PrfaH encoded by IncX3 plasmids


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 
    0.214 (Depositor), 0.217 (DCC) 
  • R-Value Work: 
    0.179 (Depositor), 0.181 (DCC) 
  • R-Value Observed: 
    0.181 (Depositor) 

Starting Model: in silico
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wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Comprehensive analysis of Enterobacteriaceae IncX plasmids reveals robust conjugation regulators PrfaH, H-NS, and conjugation-fitness tradeoff.

Yang, J.Lu, Y.Yu, J.Cai, X.Wang, C.Lv, L.Moran, R.A.Zhao, X.Hu, Z.Deng, M.Liu, J.H.

(2025) Commun Biol 8: 363-363

  • DOI: https://doi.org/10.1038/s42003-025-07782-w
  • Primary Citation of Related Structures:  
    9IK0

  • PubMed Abstract: 

    Conjugative IncX plasmids are vital for spreading clinically significant antibiotic resistance genes. We identified key factors governing the conjugative process of IncX plasmids, the plasmid encoded activator PrfaH and inhibitor H-NS. Deletion of prfaH completely abolishes conjugative transfer, and the PrfaH binding site is an ops-like sequence located downstream of the prfaH promoter. We solved the crystal structure of PrfaH and identified the residues that likely mediate interactions with its target. The IncX3 plasmid-encoded H-NS inhibits conjugation by directly repressing PrfaH expression, while simultaneously enhancing host fitness. This tradeoff between plasmid conjugation and fitness is indispensable for plasmid persistence in nutrient-deprived environments. The presence of PrfaH paralogs in various antibiotic resistance plasmids suggests its fundamental role in regulating plasmid transfer. Our study not only elucidates the regulatory mechanisms behind the horizontal transfer of IncX plasmids but also highlights PrfaH as a potential target for strategies aimed at combating antimicrobial resistance.


  • Organizational Affiliation
    • State Key Laboratory for Animal Disease Control and Prevention, Key Laboratory of Zoonosis of Ministry of Agricultural and Rural Affairs, College of Veterinary Medicine, South China Agricultural University, 510642 Guangzhou, China. yangjun@gdpu.edu.cn.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription antitermination protein RfaH
A, B
157Escherichia coliMutation(s): 0 
Gene Names: rfaHPMPNAOBH_00043
UniProt
Find proteins for A0A0C5EQ24 (Escherichia coli)
Explore A0A0C5EQ24 
Go to UniProtKB:  A0A0C5EQ24
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0C5EQ24
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free:  0.214 (Depositor), 0.217 (DCC) 
  • R-Value Work:  0.179 (Depositor), 0.181 (DCC) 
  • R-Value Observed: 0.181 (Depositor) 
Space Group: P 43
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.695α = 90
b = 57.695β = 90
c = 116.465γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China--

Revision History  (Full details and data files)

  • Version 1.0: 2025-03-19
    Type: Initial release