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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-12260 | |||||||||
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Title | Allostery through DNA drives phenotype switching | |||||||||
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![]() | Transcription-factor / DNA-binding / A-tract / Allostery / DNA BINDING PROTEIN | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 7.0 Å | |||||||||
![]() | Rosenblum G / Elad N | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Allostery through DNA drives phenotype switching. Authors: Gabriel Rosenblum / Nadav Elad / Haim Rozenberg / Felix Wiggers / Jakub Jungwirth / Hagen Hofmann / ![]() Abstract: Allostery is a pervasive principle to regulate protein function. Growing evidence suggests that also DNA is capable of transmitting allosteric signals. Yet, whether and how DNA-mediated allostery ...Allostery is a pervasive principle to regulate protein function. Growing evidence suggests that also DNA is capable of transmitting allosteric signals. Yet, whether and how DNA-mediated allostery plays a regulatory role in gene expression remained unclear. Here, we show that DNA indeed transmits allosteric signals over long distances to boost the binding cooperativity of transcription factors. Phenotype switching in Bacillus subtilis requires an all-or-none promoter binding of multiple ComK proteins. We use single-molecule FRET to demonstrate that ComK-binding at one promoter site increases affinity at a distant site. Cryo-EM structures of the complex between ComK and its promoter demonstrate that this coupling is due to mechanical forces that alter DNA curvature. Modifications of the spacer between sites tune cooperativity and show how to control allostery, which allows a fine-tuning of the dynamic properties of genetic circuits. | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 41.8 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 18 KB 18 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 10.5 KB | Display | ![]() |
Images | ![]() | 54.3 KB | ||
Masks | ![]() | 83.7 MB | ![]() | |
Filedesc metadata | ![]() | 5 KB | ||
Others | ![]() ![]() | 77.7 MB 77.7 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 1021.6 KB | Display | ![]() |
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Full document | ![]() | 1021.1 KB | Display | |
Data in XML | ![]() | 17.6 KB | Display | |
Data in CIF | ![]() | 22.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7nbnMC ![]() 6z0sC C: citing same article ( M: atomic model generated by this map |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 1.718 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_12260_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_12260_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
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Sample components
-Entire : ComK transcription factor bound to its comG promoter DNA.
Entire | Name: ComK transcription factor bound to its comG promoter DNA. |
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Components |
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-Supramolecule #1: ComK transcription factor bound to its comG promoter DNA.
Supramolecule | Name: ComK transcription factor bound to its comG promoter DNA. type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: ![]() ![]() |
-Macromolecule #1: AddAB promoter
Macromolecule | Name: AddAB promoter / type: dna / ID: 1 / Number of copies: 1 / Classification: DNA |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 24.230533 KDa |
Sequence | String: (DG)(DG)(DA)(DG)(DA)(DG)(DA)(DT)(DG)(DT) (DG)(DC)(DG)(DG)(DA)(DG)(DA)(DT)(DA)(DA) (DT)(DC)(DA)(DG)(DC)(DT)(DT)(DT)(DT) (DT)(DA)(DT)(DA)(DT)(DG)(DT)(DG)(DA)(DA) (DA) (DA)(DG)(DG)(DC)(DC)(DG) ...String: (DG)(DG)(DA)(DG)(DA)(DG)(DA)(DT)(DG)(DT) (DG)(DC)(DG)(DG)(DA)(DG)(DA)(DT)(DA)(DA) (DT)(DC)(DA)(DG)(DC)(DT)(DT)(DT)(DT) (DT)(DA)(DT)(DA)(DT)(DG)(DT)(DG)(DA)(DA) (DA) (DA)(DG)(DG)(DC)(DC)(DG)(DT)(DT) (DT)(DT)(DT)(DA)(DC)(DC)(DA)(DA)(DT)(DA) (DG)(DA) (DT)(DC)(DA)(DG)(DA)(DT)(DT) (DG)(DG)(DT)(DC)(DA)(DT)(DT)(DT)(DT)(DC) (DG) |
-Macromolecule #2: AddAB promoter
Macromolecule | Name: AddAB promoter / type: dna / ID: 2 / Number of copies: 1 / Classification: DNA |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 23.866352 KDa |
Sequence | String: (DC)(DG)(DA)(DA)(DA)(DA)(DT)(DG)(DA)(DC) (DC)(DA)(DA)(DT)(DC)(DT)(DG)(DA)(DT)(DC) (DT)(DA)(DT)(DT)(DG)(DG)(DT)(DA)(DA) (DA)(DA)(DA)(DC)(DG)(DG)(DC)(DC)(DT)(DT) (DT) (DT)(DC)(DA)(DC)(DA)(DT) ...String: (DC)(DG)(DA)(DA)(DA)(DA)(DT)(DG)(DA)(DC) (DC)(DA)(DA)(DT)(DC)(DT)(DG)(DA)(DT)(DC) (DT)(DA)(DT)(DT)(DG)(DG)(DT)(DA)(DA) (DA)(DA)(DA)(DC)(DG)(DG)(DC)(DC)(DT)(DT) (DT) (DT)(DC)(DA)(DC)(DA)(DT)(DA)(DT) (DA)(DA)(DA)(DA)(DA)(DG)(DC)(DT)(DG)(DA) (DT)(DT) (DA)(DT)(DC)(DT)(DC)(DC)(DG) (DC)(DA)(DC)(DA)(DT)(DC)(DT)(DC)(DT)(DC) (DC) |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 0.24 mg/mL | |||||||||||||||||||||
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Buffer | pH: 7 Component:
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Grid | Model: UltrAuFoil R1.2/1.3 / Support film - Material: GOLD / Support film - topology: HOLEY | |||||||||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV | |||||||||||||||||||||
Details | Monodisperse complex with dsDNA and 4 ComK equivalents. |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Detector mode: COUNTING / Average exposure time: 2.0 sec. / Average electron dose: 55.7 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 70.0 µm / Calibrated magnification: 58207 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal magnification: 105000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: FLEXIBLE FIT |
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Output model | ![]() PDB-7nbn: |