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Yorodumi- PDB-7ji0: CryoEM structure of Streptococcus thermophilus SHP pheromone rece... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7ji0 | |||||||||
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Title | CryoEM structure of Streptococcus thermophilus SHP pheromone receptor Rgg3 in complex with SHP3 | |||||||||
Components |
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Keywords | DNA BINDING PROTEIN / DNA binding transcription factor / quorum sensing / RRNPP / pheromone binding | |||||||||
Function / homology | HTH-type transcriptional regulator Rgg, C-terminal domain / Transcription activator MutR, C-terminal / Cro/C1-type HTH domain profile. / Cro/C1-type helix-turn-helix domain / Lambda repressor-like, DNA-binding domain superfamily / Tetratricopeptide-like helical domain superfamily / DNA binding / Positive transcriptional regulator MutR family Function and homology information | |||||||||
Biological species | Streptococcus thermophilus (bacteria) Streptococcus thermophilus CNRZ1066 (bacteria) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.95 Å | |||||||||
Authors | Petrou, V.I. / Capodagli, G.C. / Kaelber, J.T. / Neiditch, M.B. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Proc Natl Acad Sci U S A / Year: 2020 Title: Structure-function studies of Rgg binding to pheromones and target promoters reveal a model of transcription factor interplay. Authors: Glenn C Capodagli / Kaitlyn M Tylor / Jason T Kaelber / Vasileios I Petrou / Michael J Federle / Matthew B Neiditch / Abstract: Regulator gene of glucosyltransferase (Rgg) family proteins, such as Rgg2 and Rgg3, have emerged as primary quorum-sensing regulated transcription factors in species, controlling virulence, ...Regulator gene of glucosyltransferase (Rgg) family proteins, such as Rgg2 and Rgg3, have emerged as primary quorum-sensing regulated transcription factors in species, controlling virulence, antimicrobial resistance, and biofilm formation. Rgg2 and Rgg3 function is regulated by their interaction with oligopeptide quorum-sensing signals called short hydrophobic peptides (SHPs). The molecular basis of Rgg-SHP and Rgg-target DNA promoter specificity was unknown. To close this gap, we determined the cryoelectron microscopy (cryo-EM) structure of Rgg3 bound to its quorum-sensing signal, SHP3, and the X-ray crystal structure of Rgg3 alone. Comparison of these structures with that of an Rgg in complex with cyclosporin A (CsA), an inhibitor of SHP-induced Rgg activity, reveals the molecular basis of CsA function. Furthermore, to determine how Rgg proteins recognize DNA promoters, we determined X-ray crystal structures of both Rgg2 and Rgg3 in complex with their target DNA promoters. The physiological importance of observed Rgg-DNA interactions was dissected using in vivo genetic experiments and in vitro biochemical assays. Based on these structure-function studies, we present a revised unifying model of Rgg regulatory interplay. In contrast to existing models, where Rgg2 proteins are transcriptional activators and Rgg3 proteins are transcriptional repressors, we propose that both are capable of transcriptional activation. However, when Rgg proteins with different activation requirements compete for the same DNA promoters, those with more stringent activation requirements function as repressors by blocking promoter access of SHP-bound conformationally active Rgg proteins. While a similar gene expression regulatory scenario has not been previously described, in all likelihood it is not unique to streptococci. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7ji0.cif.gz | 88.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ji0.ent.gz | 66.2 KB | Display | PDB format |
PDBx/mmJSON format | 7ji0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7ji0_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 7ji0_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 7ji0_validation.xml.gz | 28.6 KB | Display | |
Data in CIF | 7ji0_validation.cif.gz | 39.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ji/7ji0 ftp://data.pdbj.org/pub/pdb/validation_reports/ji/7ji0 | HTTPS FTP |
-Related structure data
Related structure data | 22341MC 6w1aC 6w1eC 6w1fC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | |
EM raw data | EMPIAR-10535 (Title: Single particle cryoEM of Streptococcus thermophilus SHP pheromone receptor Rgg3 in complex with SHP3 Data size: 3.0 TB Data #1: Unaligned multi-frame micrographs of Rgg3-SHP3 complex [micrographs - multiframe]) |
-Links
-Assembly
Deposited unit |
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-Components
#1: Protein | Mass: 33242.078 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus thermophilus (strain ATCC BAA-250 / LMG 18311) (bacteria) Strain: ATCC BAA-250 / LMG 18311 / Gene: stu1044 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q5M4D0 #2: Protein/peptide | Mass: 798.969 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus thermophilus CNRZ1066 (bacteria) Production host: synthetic construct (others) |
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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: Streptococcus thermophilus SHP pheromone receptor Rgg3 in complex with SHP3 Type: COMPLEX / Entity ID: all / Source: RECOMBINANT | |||||||||||||||
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Molecular weight | Experimental value: NO | |||||||||||||||
Source (natural) | Organism: Streptococcus thermophilus (bacteria) / Organ: CNRZ1066 | |||||||||||||||
Source (recombinant) | Organism: Escherichia coli (E. coli) / Strain: BL21 (DE3) | |||||||||||||||
Buffer solution | pH: 8 | |||||||||||||||
Buffer component |
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Specimen | Conc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | |||||||||||||||
Specimen support | Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: UltrAuFoil | |||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 295 K Details: 2.5 microliters Rgg3St-SHP3 was applied to glow-discharged UltraAuFoil (1.2/1.3) 300-mesh grids (Quantifoil), blotted with filter paper for 3-3.5 s, and flash-frozen by plunging in liquid ...Details: 2.5 microliters Rgg3St-SHP3 was applied to glow-discharged UltraAuFoil (1.2/1.3) 300-mesh grids (Quantifoil), blotted with filter paper for 3-3.5 s, and flash-frozen by plunging in liquid ethane cooled with liquid nitrogen. Grids were stored in liquid nitrogen. |
-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 magnification: 130000 X / Calibrated defocus min: 500 nm / Calibrated defocus max: 3000 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 8 sec. / Electron dose: 47.13 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 2 / Num. of real images: 1464 |
EM imaging optics | Energyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV |
Image scans | Width: 3838 / Height: 3710 / Movie frames/image: 40 / Used frames/image: 1-40 |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 389743 | ||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.95 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 44069 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: REAL | ||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 6W1E Accession code: 6W1E / Source name: PDB / Type: experimental model |