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Yorodumi- PDB-7f75: Cryo-EM structure of Spx-dependent transcription activation complex -
+Open data
-Basic information
Entry | Database: PDB / ID: 7f75 | ||||||
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Title | Cryo-EM structure of Spx-dependent transcription activation complex | ||||||
Components |
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Keywords | TRANSCRIPTION/DNA / Complex / transcription activator / stress / oxidated form / TRANSCRIPTION / TRANSCRIPTION-DNA complex | ||||||
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 | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.2 Å | ||||||
Authors | Lin, W. / Feng, Y. / Shi, J. | ||||||
Funding support | 1items
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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 | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7f75.cif.gz | 636 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7f75.ent.gz | 501.1 KB | Display | PDB format |
PDBx/mmJSON format | 7f75.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7f75_validation.pdf.gz | 920.4 KB | Display | wwPDB validaton report |
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Full document | 7f75_full_validation.pdf.gz | 963.7 KB | Display | |
Data in XML | 7f75_validation.xml.gz | 87.9 KB | Display | |
Data in CIF | 7f75_validation.cif.gz | 139.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f7/7f75 ftp://data.pdbj.org/pub/pdb/validation_reports/f7/7f75 | HTTPS FTP |
-Related structure data
Related structure data | 31485MC 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
-DNA-directed RNA polymerase subunit ... , 6 types, 8 molecules ABICDEHL
#1: Protein | Mass: 34842.387 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Bacillus subtilis (bacteria) / References: UniProt: P20429, DNA-directed RNA polymerase #2: Protein | | Mass: 133847.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus subtilis (bacteria) / References: UniProt: P37870, DNA-directed RNA polymerase #3: Protein | | Mass: 134444.953 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus subtilis (bacteria) / References: UniProt: P37871, DNA-directed RNA polymerase #4: Protein | | Mass: 7766.921 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus subtilis (bacteria) / References: UniProt: O35011, DNA-directed RNA polymerase #6: Protein | | Mass: 8263.358 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus subtilis (bacteria) / References: UniProt: O31718, DNA-directed RNA polymerase #10: Protein | | Mass: 20417.891 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus subtilis (bacteria) / References: UniProt: P12464 |
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-Protein , 2 types, 2 molecules FG
#5: Protein | Mass: 43007.406 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus subtilis (bacteria) / References: UniProt: P06224 |
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#7: Protein | Mass: 15547.901 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus subtilis (bacteria) |
-TrxA promoter DNA- ... , 2 types, 2 molecules JK
#8: DNA chain | Mass: 21202.631 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Bacillus subtilis (bacteria) |
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#9: DNA chain | Mass: 20886.408 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Bacillus subtilis (bacteria) |
-Non-polymers , 2 types, 3 molecules
#11: Chemical | ChemComp-MG / |
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#12: Chemical |
-Details
Has ligand of interest | Y |
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Sequence details | The reference sequence database of chain G is GenBank WP_106610844.1 |
-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 |
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Source (natural) | Organism: Bacillus subtilis (bacteria) | ||||||||||||||||||||||||
Buffer solution | pH: 7.5 | ||||||||||||||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||
Vitrification | Cryogen name: ETHANE |
-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 |
Image recording | Electron dose: 59 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
EM software | Name: RELION / Category: final Euler assignment |
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CTF correction | Type: NONE |
3D reconstruction | Resolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 153870 / Algorithm: FOURIER SPACE / Symmetry type: POINT |