9ILL | pdb_00009ill

monomeric SarA-E89Q in complex with DNA

• PDB DOI: https://doi.org/10.2210/pdb9ILL/pdb
• NAKB: 9ILL

• Classification: DNA BINDING PROTEIN
• Organism(s): Staphylococcus aureus subsp. aureus N315, synthetic construct
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2024-06-30 Released: 2025-10-15 
• Deposition Author(s): Xia, B., Fu, D.H.
• Funding Organization(s): National Basic Research Program of China (973 Program)

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 20 
• Selection Criteria: structures with the lowest energy 

Literature

solution Structure of the monomeric SarA in complex with DNA

Xia, B., Fu, D.H.

(2023) Biomol NMR Assign 17: 193-197

• PubMed: 37405582 
• DOI: https://doi.org/10.1007/s12104-023-10140-8
• Primary Citation of Related Structures:  
  9ILL


• PubMed Abstract: 
  

  SarA is a global transcription regulator in S. aureus which regulates the expression of over 120 genes related to quorum sensing, biofilm synthesis, drug resistance and many other important physiological processes during host infection. SarA can bind to the promoter region of agr and other target genes to activate or repress the transcription. The crystal structure of SarA uncovered a MarR protein-like conformation with two symmetrical winged helix domains, while its DNA binding mechanism is still unknown. We have constructed a monomeric DNA binding domain of SarA (SarA ^ΔN19 ) for the study of the interaction between SarA and DNA with NMR spectroscopy. Here, we report the ¹ H, ¹³ C and ¹⁵ N NMR assignment of SarA ^ΔN19 /DNA complex which is the first step towards further structure and function analysis.

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Organizational Affiliation: 
• Beijing Nuclear Magnetic Resonance Center, College of Chemistry and Molecular Engineering, School of Life Sciences, Peking University, Beijing, China.
Institute of Biophysics, Chinese Academy of Science, Beijing, 100101, China.
Beijing Nuclear Magnetic Resonance Center, College of Chemistry and Molecular Engineering, School of Life Sciences, Peking University, Beijing, China. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: NMR Distance Restraints

Macromolecule Content 

• Total Structure Weight: 24.83 kDa 
• Atom Count: 1,704 
• Modeled Residue Count: 150 
• Deposited Residue Count: 150 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcriptional regulator SarA	A	114	Staphylococcus aureus subsp. aureus N315	Mutation(s): 1  Gene Names: sarA, SA0573
UniProt
Find proteins for Q2G2U9 (Staphylococcus aureus (strain NCTC 8325 / PS 47)) Explore Q2G2U9  Go to UniProtKB:  Q2G2U9

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA	B, C	18	synthetic construct

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 20 
• Selection Criteria: structures with the lowest energy 

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-10-15 
Deposition Author(s): Xia, B., Fu, D.H.

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Funding Organization	Location	Grant Number
National Basic Research Program of China (973 Program)	China	--

Revision History  

• Version 1.0: 2025-10-15
  Type: Initial release