+Open data
-Basic information
Entry | Database: PDB / ID: 8dq1 | |||||||||||||||
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Title | Quorum-sensing receptor RhlR bound to PqsE | |||||||||||||||
Components |
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Keywords | TRANSCRIPTION/DNA / transcriptional regulators / quorum sensing / DNA binding / TRANSCRIPTION-DNA complex | |||||||||||||||
Function / homology | Function and homology information 2-aminobenzoylacetyl-CoA thioesterase / secondary metabolite biosynthetic process / hydrolase activity / regulation of DNA-templated transcription / DNA binding / metal ion binding Similarity search - Function | |||||||||||||||
Biological species | Pseudomonas aeruginosa (bacteria) | |||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.1 Å | |||||||||||||||
Authors | Paczkowski, J.E. / Fromme, J.C. / Feathers, J.R. | |||||||||||||||
Funding support | United States, 4items
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Citation | Journal: Structure / Year: 2022 Title: Structure of the RhlR-PqsE complex from Pseudomonas aeruginosa reveals mechanistic insights into quorum-sensing gene regulation. Authors: J Ryan Feathers / Erica K Richael / Kayla A Simanek / J Christopher Fromme / Jon E Paczkowski / Abstract: Pseudomonas aeruginosa is an opportunistic pathogen that is responsible for thousands of deaths every year in the United States. P. aeruginosa virulence factor production is mediated by quorum ...Pseudomonas aeruginosa is an opportunistic pathogen that is responsible for thousands of deaths every year in the United States. P. aeruginosa virulence factor production is mediated by quorum sensing, a mechanism of bacterial cell-cell communication that relies on the production and detection of signal molecules called autoinducers. In P. aeruginosa, the transcription factor receptor RhlR is activated by a RhlI-synthesized autoinducer. We recently showed that RhlR-dependent transcription is enhanced by a physical interaction with the enzyme PqsE via increased affinity of RhlR for promoter DNA. However, the molecular basis for complex formation and how complex formation enhanced RhlR transcriptional activity remained unclear. Here, we report the structure of ligand-bound RhlR in complex with PqsE. Additionally, we determined the structure of the complex bound with DNA, revealing the mechanism by which RhlR-mediated transcription is enhanced by PqsE, thereby establishing the molecular basis for RhlR-dependent virulence factor production in P. aeruginosa. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8dq1.cif.gz | 414.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8dq1.ent.gz | 332.3 KB | Display | PDB format |
PDBx/mmJSON format | 8dq1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8dq1_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 8dq1_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 8dq1_validation.xml.gz | 44 KB | Display | |
Data in CIF | 8dq1_validation.cif.gz | 67.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dq/8dq1 ftp://data.pdbj.org/pub/pdb/validation_reports/dq/8dq1 | HTTPS FTP |
-Related structure data
Related structure data | 27646MC 8dq0C C: citing same article (ref.) M: map data used to model this data |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 27611.596 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: A9JPX4 #2: Protein | Mass: 34350.297 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: P20581 #3: DNA chain | | Mass: 5470.558 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Pseudomonas aeruginosa (bacteria) #4: DNA chain | | Mass: 5563.588 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Pseudomonas aeruginosa (bacteria) #5: Chemical | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Tetrameric complex of RhlR:mBTL bound to PqsE / Type: COMPLEX / Entity ID: #1-#4 / Source: RECOMBINANT |
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Molecular weight | Value: .123 MDa / Experimental value: NO |
Source (natural) | Organism: Pseudomonas aeruginosa (bacteria) |
Source (recombinant) | Organism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) |
Buffer solution | pH: 8 |
Specimen | Conc.: 5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |
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Microscopy | Model: FEI TALOS ARCTICA |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 1500 nm / Nominal defocus min: 800 nm |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.18.2_3874: / Classification: refinement | ||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 84842 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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