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- EMDB-20781: Structural basis for control of antibiotic production by bacteria... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-20781 | |||||||||
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Title | Structural basis for control of antibiotic production by bacterial hormones | |||||||||
![]() | Map file - Postprocess masked .mrc UCSF Chimera 1.11, visualization -Volume viewer step 1 -Contour level 0.0181 | |||||||||
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Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.2 Å | |||||||||
![]() | Bhukya H | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Molecular basis for control of antibiotic production by a bacterial hormone. Authors: Shanshan Zhou / Hussain Bhukya / Nicolas Malet / Peter J Harrison / Dean Rea / Matthew J Belousoff / Hariprasad Venugopal / Paulina K Sydor / Kathryn M Styles / Lijiang Song / Max J Cryle / ...Authors: Shanshan Zhou / Hussain Bhukya / Nicolas Malet / Peter J Harrison / Dean Rea / Matthew J Belousoff / Hariprasad Venugopal / Paulina K Sydor / Kathryn M Styles / Lijiang Song / Max J Cryle / Lona M Alkhalaf / Vilmos Fülöp / Gregory L Challis / Christophe Corre / ![]() ![]() Abstract: Actinobacteria produce numerous antibiotics and other specialized metabolites that have important applications in medicine and agriculture. Diffusible hormones frequently control the production of ...Actinobacteria produce numerous antibiotics and other specialized metabolites that have important applications in medicine and agriculture. Diffusible hormones frequently control the production of such metabolites by binding TetR family transcriptional repressors (TFTRs), but the molecular basis for this remains unclear. The production of methylenomycin antibiotics in Streptomyces coelicolor A3(2) is initiated by the binding of 2-alkyl-4-hydroxymethylfuran-3-carboxylic acid (AHFCA) hormones to the TFTR MmfR. Here we report the X-ray crystal structure of an MmfR-AHFCA complex, establishing the structural basis for hormone recognition. We also elucidate the mechanism for DNA release upon hormone binding through the single-particle cryo-electron microscopy structure of an MmfR-operator complex. DNA binding and release assays with MmfR mutants and synthetic AHFCA analogues define the role of individual amino acid residues and hormone functional groups in ligand recognition and DNA release. These findings will facilitate the exploitation of actinobacterial hormones and their associated TFTRs in synthetic biology and in the discovery of new antibiotics. | |||||||||
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 | ![]() | 3.1 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 18.3 KB 18.3 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 6.5 KB | Display | ![]() |
Images | ![]() | 50 KB | ||
Masks | ![]() | 22.2 MB | ![]() | |
Others | ![]() ![]() | 17.1 MB 17.1 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 429 KB | Display | ![]() |
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Full document | ![]() | 428.6 KB | Display | |
Data in XML | ![]() | 12.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
EMDB pages | ![]() ![]() |
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Map
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Annotation | Map file - Postprocess masked .mrc UCSF Chimera 1.11, visualization -Volume viewer step 1 -Contour level 0.0181 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.092 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: Half map file - run half1 class001 unfil.mrc UCSF Chimera 1.11,...
File | emd_20781_half_map_1.map | ||||||||||||
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Annotation | Half map file - run_half1_class001_unfil.mrc UCSF Chimera 1.11, visualization -Volume viewer step 1 -Contour level 0.017 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map file - run half2 class001 unfil.mrc UCSF Chimera 1.11,...
File | emd_20781_half_map_2.map | ||||||||||||
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Annotation | Half map file - run_half2_class001_unfil.mrc UCSF Chimera 1.11, visualization -Volume viewer step 1 -Contour level 0.017 | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : protein-DNA complex
Entire | Name: protein-DNA complex |
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Components |
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-Supramolecule #1: protein-DNA complex
Supramolecule | Name: protein-DNA complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all Details: protein-DNA complex. two homodimers of protein bound to a double stranded DNA |
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Source (natural) | Organism: ![]() |
Recombinant expression | Organism: ![]() ![]() |
Molecular weight | Experimental: 114 KDa |
-Macromolecule #1: protein MmfR
Macromolecule | Name: protein MmfR / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MHHHHHHGKP IPNPLLGLDS TENLYFQGID PFTMTSAQQP TPFAVRSNVP RGPHPQQERS IKTRAQILEA ASEIFASRGY RGASVKDVAE RVGMTKGAVY FHFPSKESLA IAVVEEHYAR WPAAMEEIRI QGFTPLETVE EMLHRAAQAF RDDPVMQAGA RLQSERAFID ...String: MHHHHHHGKP IPNPLLGLDS TENLYFQGID PFTMTSAQQP TPFAVRSNVP RGPHPQQERS IKTRAQILEA ASEIFASRGY RGASVKDVAE RVGMTKGAVY FHFPSKESLA IAVVEEHYAR WPAAMEEIRI QGFTPLETVE EMLHRAAQAF RDDPVMQAGA RLQSERAFID AELPLPYVDW THLLEVPLQD AREAGQLRAG VDPAAAARSL VAAFFGMQHV SDNLHQRADI MERWQELREL MFFALRA |
-Macromolecule #2: synthetic DNA
Macromolecule | Name: synthetic DNA / type: dna / ID: 2 / Details: 5'-ATACCTGCGGGAAGGTATT-3' / Classification: DNA |
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Source (natural) | Organism: ![]() |
Sequence | String: ATACCTGCGG GAAGGTATT |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 0.08 mg/mL | |||||||||
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Buffer | pH: 8 Component:
Details: 20 mM tris pH 8.0 and 200 mM NaCl fresh and autoclaved | |||||||||
Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER | |||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK III | |||||||||
Details | protein-DNA complex |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Phase plate: VOLTA PHASE PLATE / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Frames/image: 1-50 / Number grids imaged: 2 / Average exposure time: 10.0 sec. / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus min: -0.0005 µm / Nominal magnification: 165000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
-Atomic model buiding 1
Refinement | Protocol: FLEXIBLE FIT / Overall B value: 214 |
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