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- PDB-8r7y: Deoxyribonucleoside regulator DeoR in complex with the DNA operator -
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Open data
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Basic information
Entry | Database: PDB / ID: 8r7y | ||||||
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Title | Deoxyribonucleoside regulator DeoR in complex with the DNA operator | ||||||
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![]() | DNA BINDING PROTEIN / transcriptional repressor / protein-DNA complex / Bacillus subtilis | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Pachl, P. / Soltysova, M. / Rezacova, P. | ||||||
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. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 305 KB | Display | ![]() |
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PDB format | ![]() | 233.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 8r3gC 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: ASP / End label comp-ID: ASP / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 1 - 312 / Label seq-ID: 6 - 317
NCS ensembles :
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Components
#1: Protein | Mass: 35796.676 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: The N-terminal GIDPFT sequence is a cloning artefact. Source: (gene. exp.) ![]() ![]() Gene: deoR / Production host: ![]() ![]() #2: DNA chain | Mass: 5519.612 Da / Num. of mol.: 2 / Source method: obtained synthetically Source: (synth.) ![]() ![]() #3: DNA chain | Mass: 5506.630 Da / Num. of mol.: 2 / Source method: obtained synthetically Source: (synth.) ![]() ![]() #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.22 Å3/Da / Density % sol: 70.6 % / Description: Thin needle-shaped crystal. |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6.3 Details: The volume ratio of the protein/DNA solution and precipitant solution - 1:2 Precipitant solution: 50 mM sodium cacodylate, pH 6.3, 75 mM CaCl2, 25 mM MgCl2, 3.5% (v/v) PEG 2K Crystal was ...Details: The volume ratio of the protein/DNA solution and precipitant solution - 1:2 Precipitant solution: 50 mM sodium cacodylate, pH 6.3, 75 mM CaCl2, 25 mM MgCl2, 3.5% (v/v) PEG 2K Crystal was cryo-protected by a quick soaking in 25% (v/v) glycerol. Temp details: Grown in an air-conditioned room. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 31, 2018 | ||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9141 Å / Relative weight: 1 | ||||||||||||||||||||||||||||
Reflection | Resolution: 3.6→50 Å / Num. obs: 32081 / % possible obs: 98.9 % / Redundancy: 13.1 % / Biso Wilson estimate: 122.8 Å2 / CC1/2: 0.993 / Rrim(I) all: 0.748 / Net I/σ(I): 4.86 | ||||||||||||||||||||||||||||
Reflection shell |
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Processing
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Refinement | Method to determine structure: ![]() Details: Hydrogens have been used if present in the input file
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 172.198 Å2
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Refinement step | Cycle: LAST / Resolution: 3.7→48.924 Å
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Refine LS restraints |
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Refine LS restraints NCS | Auth asym-ID: A / Refine-ID: X-RAY DIFFRACTION / Type: medium positional; mediume thermal / Weight Biso : 2 / Weight position: 0.5
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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