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Yorodumi- EMDB-31485: Cryo-EM structure of Spx-dependent transcription activation complex -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-31485 | |||||||||
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Title | Cryo-EM structure of Spx-dependent transcription activation complex | |||||||||
Map data | ||||||||||
Sample |
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Function / homology | Function and homology information nucleoid / sigma factor activity / DNA-directed RNA polymerase complex / DNA-templated transcription initiation / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / protein dimerization activity / response to antibiotic / DNA-templated transcription ...nucleoid / sigma factor activity / DNA-directed RNA polymerase complex / DNA-templated transcription initiation / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / protein dimerization activity / response to antibiotic / DNA-templated transcription / regulation of DNA-templated transcription / magnesium ion binding / DNA binding / zinc ion binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Bacillus subtilis (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.2 Å | |||||||||
Authors | Lin W / Feng Y / Shi J | |||||||||
Funding support | 1 items
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Citation | Journal: Nucleic Acids Res / Year: 2021 Title: Structural basis of transcription activation by the global regulator Spx. Authors: Jing Shi / Fangfang Li / Aijia Wen / Libing Yu / Lu Wang / Fulin Wang / Yuanling Jin / Sha Jin / Yu Feng / Wei Lin / Abstract: Spx is a global transcriptional regulator in Gram-positive bacteria and has been inferred to efficiently activate transcription upon oxidative stress by engaging RNA polymerase (RNAP) and promoter ...Spx is a global transcriptional regulator in Gram-positive bacteria and has been inferred to efficiently activate transcription upon oxidative stress by engaging RNA polymerase (RNAP) and promoter DNA. However, the precise mechanism by which it interacts with RNAP and promoter DNA to initiate transcription remains obscure. Here, we report the cryo-EM structure of an intact Spx-dependent transcription activation complex (Spx-TAC) from Bacillus subtilis at 4.2 Å resolution. The structure traps Spx in an active conformation and defines key interactions accounting for Spx-dependent transcription activation. Strikingly, an oxidized Spx monomer engages RNAP by simultaneously interacting with the C-terminal domain of RNAP alpha subunit (αCTD) and σA. The interface between Spx and αCTD is distinct from those previously reported activators, indicating αCTD as a multiple target for the interaction between RNAP and various transcription activators. Notably, Spx specifically wraps the conserved -44 element of promoter DNA, thereby stabilizing Spx-TAC. Besides, Spx interacts extensively with σA through three different interfaces and promotes Spx-dependent transcription activation. Together, our structural and biochemical results provide a novel mechanistic framework for the regulation of bacterial transcription activation and shed new light on the physiological roles of the global Spx-family transcription factors. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_31485.map.gz | 28.4 MB | EMDB map data format | |
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Header (meta data) | emd-31485-v30.xml emd-31485.xml | 22.8 KB 22.8 KB | Display Display | EMDB header |
Images | emd_31485.png | 81.4 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-31485 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-31485 | HTTPS FTP |
-Validation report
Summary document | emd_31485_validation.pdf.gz | 485.1 KB | Display | EMDB validaton report |
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Full document | emd_31485_full_validation.pdf.gz | 484.7 KB | Display | |
Data in XML | emd_31485_validation.xml.gz | 5.6 KB | Display | |
Data in CIF | emd_31485_validation.cif.gz | 6.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-31485 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-31485 | HTTPS FTP |
-Related structure data
Related structure data | 7f75MC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_31485.map.gz / Format: CCP4 / Size: 30.5 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: 1.307 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
+Entire : Bacillus subtilis Spx dependent transcription activation complex
+Supramolecule #1: Bacillus subtilis Spx dependent transcription activation complex
+Supramolecule #2: Spx-dependent transcription activation complex
+Supramolecule #3: DNA
+Macromolecule #1: DNA-directed RNA polymerase subunit alpha
+Macromolecule #2: DNA-directed RNA polymerase subunit beta
+Macromolecule #3: DNA-directed RNA polymerase subunit beta'
+Macromolecule #4: DNA-directed RNA polymerase subunit omega
+Macromolecule #5: RNA polymerase sigma factor SigA
+Macromolecule #6: DNA-directed RNA polymerase subunit epsilon
+Macromolecule #7: transcriptional regulator Spx
+Macromolecule #10: DNA-directed RNA polymerase subunit delta
+Macromolecule #8: trxA promoter DNA-Non template strand
+Macromolecule #9: trxA promoter DNA-template strand
+Macromolecule #11: MAGNESIUM ION
+Macromolecule #12: ZINC ION
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 59.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: PDB ENTRY PDB model - PDB ID: |
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Final reconstruction | Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 153870 |
Initial angle assignment | Type: ANGULAR RECONSTITUTION |
Final angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: RELION |