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Open data
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Basic information
Entry | Database: PDB / ID: 8r3g | |||||||||
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Title | Central glycolytic genes regulator (CggR) bound to DNA operator | |||||||||
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![]() | DNA BINDING PROTEIN / Bacillus subtilis / transcription repressor / glucose catabolism / SorC family | |||||||||
Function / homology | ![]() | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.4 Å | |||||||||
![]() | Skerlova, J. / Soltysova, M. / Rezacova, P. / Skubnik, K. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural characterization of two prototypical repressors of SorC family reveals tetrameric assemblies on DNA and mechanism of function. Authors: Markéta Šoltysová / Jana Škerlová / Petr Pachl / Karel Škubník / Milan Fábry / Irena Sieglová / Martina Farolfi / Irina Grishkovskaya / Michal Babiak / Jiří Nováček / Libor ...Authors: Markéta Šoltysová / Jana Škerlová / Petr Pachl / Karel Škubník / Milan Fábry / Irena Sieglová / Martina Farolfi / Irina Grishkovskaya / Michal Babiak / Jiří Nováček / Libor Krásný / Pavlína Řezáčová / ![]() Abstract: The SorC family of transcriptional regulators plays a crucial role in controlling the carbohydrate metabolism and quorum sensing. We employed an integrative approach combining X-ray crystallography ...The SorC family of transcriptional regulators plays a crucial role in controlling the carbohydrate metabolism and quorum sensing. We employed an integrative approach combining X-ray crystallography and cryo-electron microscopy to investigate architecture and functional mechanism of two prototypical representatives of two sub-classes of the SorC family: DeoR and CggR from Bacillus subtilis. Despite possessing distinct DNA-binding domains, both proteins form similar tetrameric assemblies when bound to their respective DNA operators. Structural analysis elucidates the process by which the CggR-regulated gapA operon is derepressed through the action of two effectors: fructose-1,6-bisphosphate and newly confirmed dihydroxyacetone phosphate. Our findings provide the first comprehensive understanding of the DNA binding mechanism of the SorC-family proteins, shedding new light on their functional characteristics. | |||||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 302.1 KB | Display | ![]() |
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PDB format | ![]() | 238.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 57.1 KB | Display | |
Data in CIF | ![]() | 83.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 18864MC ![]() 8r7yC M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Components
#1: Protein | Mass: 38623.496 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: N-terminal amino-acid sequence GIDPFT remains a part of the protein upon TEV cleavage as a cloning artefact. Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: DNA chain | | Mass: 13780.870 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: Only 41bp were modelled into the electron density map (two base pairs at both ends are missing). Source: (synth.) ![]() ![]() #3: DNA chain | | Mass: 13931.952 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: Only 41bp were modelled into the electron density map (two base pairs at both sides are missing). Source: (synth.) ![]() ![]() Has ligand of interest | N | |
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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 |
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Sample preparation
Component | Name: A complex of Central glycolytic genes regulator (CggR) from Bacillus subtilis and the DNA operator (OLR). Type: COMPLEX Details: A complex of full-length CggR with its 45bp DNA operator. Entity ID: all / Source: RECOMBINANT | ||||||||||||||||||||
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Molecular weight | Experimental value: NO | ||||||||||||||||||||
Source (natural) | Organism: ![]() ![]() | ||||||||||||||||||||
Source (recombinant) | Organism: ![]() ![]() | ||||||||||||||||||||
Buffer solution | pH: 7.5 Details: 20 mM Tris-HCl, pH 7.5, 100 mM NaCl and 0.02% (v/v) beta-mercaptoethanol | ||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 0.86 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid type: C-flat | ||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 165000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 1500 nm / Cs: 2.7 mm / C2 aperture diameter: 30 µm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 40 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 QUANTUM (4k x 4k) |
EM imaging optics | Energyfilter name: GIF Quantum LS / Energyfilter slit width: 20 eV |
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Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||||||||||||||
3D reconstruction | Resolution: 4.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 220146 / Algorithm: FOURIER SPACE / Symmetry type: POINT | |||||||||||||||||||||
Atomic model building | B value: 24.32 / Protocol: RIGID BODY FIT / Space: REAL Details: Rigid body fitting of starting PDB models in Phenix and Coot was combined with manual rebuilding of certain model regions in Coot. | |||||||||||||||||||||
Atomic model building |
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