9LLQ | pdb_00009llq

Structure of TetR2 and DNA probe


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 
    0.269 (Depositor), 0.270 (DCC) 
  • R-Value Work: 
    0.223 (Depositor), 0.224 (DCC) 
  • R-Value Observed: 
    0.228 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


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Literature

Structural and mechanistic insights into the transcriptional regulation of chromosomal T6SS by large conjugative plasmid-encoded TetRs in Acinetobacter baumannii.

He, W.Ouyang, Z.Zhang, J.Guo, X.Jiao, M.Qin, Q.He, X.Kang, L.Hwang, P.M.Zheng, F.Zhang, G.Wen, Y.

(2025) Nucleic Acids Res 53

  • DOI: https://doi.org/10.1093/nar/gkaf755
  • Primary Citation of Related Structures:  
    8Z6D, 8Z6E, 9LLQ

  • PubMed Abstract: 

    The type VI secretion system (T6SS) is a highly sophisticated nanomachine widely used by bacteria to achieve competitive advantage, important for survival and pathogenicity. In Acinetobacter baumannii, the large conjugative plasmid pAB3 encodes two TetR-family transcriptional regulators, TetR1 and TetR2, that play crucial roles in restricting T6SS function and promoting recipient survival after conjugation. Using X-ray crystallography, we demonstrate that the plasmid-encoded TetRs are structurally homologous but distinct in DNA sequence binding preferences, which we have also mapped out using chromatin immunoprecipitation and validated with electrophoretic mobility shift assay and isothermal titration calorimetry. Transcriptomics and functional studies demonstrated that TetR1 and TetR2 collaboratively downregulate most of the components of the T6SS, but they also impact metabolic pathways and biofilm formation, having an impact on cell morphology, invasiveness, and virulence in a mouse infection model. Taken together, this work provides structural and mechanistic insights into the widespread regulatory influence of plasmid-encoded TetR1 and TetR2 in A. baumannii, providing new insights into plasmid-chromosome cross-regulating pathways and enlightening antimicrobial drug discovery targeting A. baumannii.


  • Organizational Affiliation
    • Center for Microbiome Research of Med-X Institute, Department of Critical Care Medicine, Shaanxi Provincial Key Laboratory of Sepsis in Critical Care Medicine, The First Affiliated Hospital, Xi'an Jiaotong University, Xi'an 710061, China.

Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
TetR family transcriptional regulator
A, B
191Acinetobacter baumanniiMutation(s): 0 
Gene Names: AUO97_08420EKS29_16065F4T85_12235FJU42_13590
UniProt
Find proteins for A0A7U3XWK7 (Acinetobacter baumannii (strain ACICU))
Explore A0A7U3XWK7 
Go to UniProtKB:  A0A7U3XWK7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A7U3XWK7
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains LengthOrganismImage
DNA (5'-D(P*AP*AP*AP*AP*AP*GP*AP*CP*TP*AP*AP*TP*CP*TP*GP*TP*CP*TP*AP*TP*CP*TP*AP*T)-3')C [auth E]24Acinetobacter baumannii
Sequence Annotations
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  • Reference Sequence

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Entity ID: 3
MoleculeChains LengthOrganismImage
DNA (5'-D(P*AP*TP*AP*GP*AP*TP*AP*GP*AP*CP*AP*GP*AP*TP*TP*AP*GP*TP*CP*TP*TP*TP*TP*T)-3')D [auth F]24Acinetobacter baumannii
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free:  0.269 (Depositor), 0.270 (DCC) 
  • R-Value Work:  0.223 (Depositor), 0.224 (DCC) 
  • R-Value Observed: 0.228 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 109.023α = 90
b = 116.521β = 90
c = 113.12γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
autoPXdata reduction
Aimlessdata scaling
PHENIXphasing

Structure Validation

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Entry History & Funding Information

Deposition Data

  • Released Date: 2025-08-27 
  • Deposition Author(s): He, W., Wen, Y.

Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)ChinaNo.82072237

Revision History  (Full details and data files)

  • Version 1.0: 2025-08-27
    Type: Initial release