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Yorodumi- EMDB-18864: Central glycolytic genes regulator (CggR) bound to DNA operator -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-18864 | |||||||||
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Title | Central glycolytic genes regulator (CggR) bound to DNA operator | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Bacillus subtilis / transcription repressor / glucose catabolism / SorC family / DNA BINDING PROTEIN | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Bacillus subtilis (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.4 Å | |||||||||
Authors | Skerlova J / Soltysova M / Rezacova P / Skubnik K | |||||||||
Funding support | Czech Republic, European Union, 2 items
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Citation | Journal: Nucleic Acids Res / Year: 2024 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
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_18864.map.gz | 156.8 MB | EMDB map data format | |
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Header (meta data) | emd-18864-v30.xml emd-18864.xml | 20.1 KB 20.1 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_18864_fsc.xml | 12.5 KB | Display | FSC data file |
Images | emd_18864.png | 78.8 KB | ||
Masks | emd_18864_msk_1.map | 166.4 MB | Mask map | |
Filedesc metadata | emd-18864.cif.gz | 7.1 KB | ||
Others | emd_18864_half_map_1.map.gz emd_18864_half_map_2.map.gz | 154.6 MB 154.6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-18864 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-18864 | HTTPS FTP |
-Validation report
Summary document | emd_18864_validation.pdf.gz | 817.4 KB | Display | EMDB validaton report |
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Full document | emd_18864_full_validation.pdf.gz | 817 KB | Display | |
Data in XML | emd_18864_validation.xml.gz | 20 KB | Display | |
Data in CIF | emd_18864_validation.cif.gz | 26.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-18864 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-18864 | HTTPS FTP |
-Related structure data
Related structure data | 8r3gMC 8r7yC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_18864.map.gz / Format: CCP4 / Size: 166.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.822 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_18864_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_18864_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_18864_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : A complex of Central glycolytic genes regulator (CggR) from Bacil...
Entire | Name: A complex of Central glycolytic genes regulator (CggR) from Bacillus subtilis and the DNA operator (OLR). |
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Components |
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-Supramolecule #1: A complex of Central glycolytic genes regulator (CggR) from Bacil...
Supramolecule | Name: A complex of Central glycolytic genes regulator (CggR) from Bacillus subtilis and the DNA operator (OLR). type: complex / ID: 1 / Parent: 0 / Macromolecule list: all Details: A complex of full-length CggR with its 45bp DNA operator. |
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Source (natural) | Organism: Bacillus subtilis (bacteria) / Location in cell: cytoplasm |
-Macromolecule #1: Central glycolytic genes regulator
Macromolecule | Name: Central glycolytic genes regulator / type: protein_or_peptide / ID: 1 Details: N-terminal amino-acid sequence GIDPFT remains a part of the protein upon TEV cleavage as a cloning artefact. Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: Bacillus subtilis (bacteria) / Cell: Bacterium |
Molecular weight | Theoretical: 38.623496 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: GIDPFT(MSE)NQL IQAQKKLLPD LLLV(MSE)QKRFE ILQYIRLTEP IGRRSLSASL GISERVLRGE VQFLKEQNLV DI KTNG(MSE)TL TEEGYELLSV LEDT(MSE)KDVLG LTLLEKTLKE RLNLKDAIIV SGDSDQSPWV KKE(MSE)GRAAVA C (MSE)KKRFSGK ...String: GIDPFT(MSE)NQL IQAQKKLLPD LLLV(MSE)QKRFE ILQYIRLTEP IGRRSLSASL GISERVLRGE VQFLKEQNLV DI KTNG(MSE)TL TEEGYELLSV LEDT(MSE)KDVLG LTLLEKTLKE RLNLKDAIIV SGDSDQSPWV KKE(MSE)GRAAVA C (MSE)KKRFSGK NIVAVTGGTT IEAVAE(MSE)(MSE)TP DSKNRELLFV PARGGLGEDV KNQANTICAH (MSE)AEKAS GTY RLLFVPGQLS QGAYSSIIEE PSVKEVLNTI KSAS(MSE)LVHGI GEAKT(MSE)AQRR NTPLEDLKKI DDNDAVTEA FGYYFNADGE VVHKVHSVG(MSE) QLDDIDAIPD IIAVAGGSSK AEAIEAYFKK PRNTVLVTDE GAAKKLLRDE UniProtKB: Central glycolytic genes regulator |
-Macromolecule #2: operator DNA
Macromolecule | Name: operator DNA / type: dna / ID: 2 Details: Only 41bp were modelled into the electron density map (two base pairs at both ends are missing). Number of copies: 1 / Classification: DNA |
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Source (natural) | Organism: Bacillus subtilis (bacteria) |
Molecular weight | Theoretical: 13.78087 KDa |
Sequence | String: (DT)(DT)(DG)(DC)(DT)(DG)(DG)(DA)(DC)(DA) (DT)(DT)(DA)(DT)(DA)(DT)(DG)(DT)(DC)(DC) (DC)(DG)(DC)(DT)(DA)(DT)(DG)(DA)(DC) (DA)(DA)(DA)(DA)(DA)(DA)(DC)(DG)(DT)(DC) (DC) (DC)(DG)(DT)(DC)(DA) |
-Macromolecule #3: operator DNA
Macromolecule | Name: operator DNA / type: dna / ID: 3 Details: Only 41bp were modelled into the electron density map (two base pairs at both sides are missing). Number of copies: 1 / Classification: DNA |
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Source (natural) | Organism: Bacillus subtilis (bacteria) |
Molecular weight | Theoretical: 13.931952 KDa |
Sequence | String: (DT)(DG)(DA)(DC)(DG)(DG)(DG)(DA)(DC)(DG) (DT)(DT)(DT)(DT)(DT)(DT)(DG)(DT)(DC)(DA) (DT)(DA)(DG)(DC)(DG)(DG)(DG)(DA)(DC) (DA)(DT)(DA)(DT)(DA)(DA)(DT)(DG)(DT)(DC) (DC) (DA)(DG)(DC)(DA)(DA) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.86 mg/mL | ||||||||||||
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Buffer | pH: 7.5 Component:
Details: 20 mM Tris-HCl, pH 7.5, 100 mM NaCl and 0.02% (v/v) beta-mercaptoethanol | ||||||||||||
Grid | Model: C-flat / Material: COPPER / Pretreatment - Type: GLOW DISCHARGE | ||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: COUNTING / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 30.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 165000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Initial model |
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Details | Rigid body fitting of starting PDB models in Phenix and Coot was combined with manual rebuilding of certain model regions in Coot. | ||||||
Refinement | Space: REAL / Protocol: RIGID BODY FIT / Overall B value: 24.32 | ||||||
Output model | PDB-8r3g: |