+Open data
-Basic information
Entry | Database: PDB / ID: 6z0s | ||||||
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Title | Allostery through DNA drives phenotype switching | ||||||
Components |
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Keywords | DNA BINDING PROTEIN / Transcription-factor / DNA-binding / A-tract / Allostery | ||||||
Function / homology | DNA / DNA (> 10) Function and homology information | ||||||
Biological species | Bacillus subtilis (bacteria) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 5.7 Å | ||||||
Authors | Rosenblum, G. / Elad, N. / Rozenberg, H. / Wiggers, F. / Jungwirth, J. / Hofmann, H. | ||||||
Funding support | Israel, 1items
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Citation | Journal: Nat Commun / Year: 2021 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 |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6z0s.cif.gz | 87.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6z0s.ent.gz | 61.6 KB | Display | PDB format |
PDBx/mmJSON format | 6z0s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z0/6z0s ftp://data.pdbj.org/pub/pdb/validation_reports/z0/6z0s | HTTPS FTP |
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-Related structure data
Related structure data | 11022MC 7nbnC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: DNA chain | Mass: 28476.242 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: 84-mer modeled upon 93 nucleotides / Source: (synth.) Bacillus subtilis (bacteria) |
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#2: DNA chain | Mass: 28882.619 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: 86-mer modeled upon 93 nucleotides / Source: (synth.) Bacillus subtilis (bacteria) |
-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: ComK transcription factor bound to its comG promoter DNA. Type: COMPLEX / Entity ID: all / Source: RECOMBINANT | |||||||||||||||||||||||||||||||||||
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Molecular weight | Experimental value: NO | |||||||||||||||||||||||||||||||||||
Source (natural) | Organism: Bacillus subtilis (bacteria) | |||||||||||||||||||||||||||||||||||
Source (recombinant) | Organism: Synthetic construct (others) | |||||||||||||||||||||||||||||||||||
Buffer solution | pH: 7 | |||||||||||||||||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 0.24 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES Details: Monodisperse complex with dsDNA and 4 ComK equivalents. | |||||||||||||||||||||||||||||||||||
Specimen support | Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: UltrAuFoil R1.2/1.3 | |||||||||||||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K |
-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: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 105000 X / Calibrated magnification: 58207 X / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 2 sec. / Electron dose: 55.7 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.19_4092: / Classification: refinement | ||||||||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 5.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 88140 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: REAL | ||||||||||||||||||||||||||||||||
Refine LS restraints |
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