[English] 日本語
![](img/lk-miru.gif)
- PDB-7w5x: Cryo-EM structure of SoxS-dependent transcription activation comp... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 7w5x | ||||||
---|---|---|---|---|---|---|---|
Title | Cryo-EM structure of SoxS-dependent transcription activation complex with zwf promoter DNA | ||||||
![]() |
| ||||||
![]() | TRANSCRIPTION/DNA / bacterial RNA polymerase / TRANSCRIPTION-DNA COMPLEX | ||||||
Function / homology | ![]() bacterial-type RNA polymerase holo enzyme binding / sigma factor antagonist complex / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Lin, W. / Feng, Y. / Shi, J. | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() Title: Structural basis of three different transcription activation strategies adopted by a single regulator SoxS. Authors: Jing Shi / Lu Wang / Aijia Wen / Fulin Wang / Yuqiong Zhang / Libing Yu / Fangfang Li / Yuanling Jin / Zhenzhen Feng / Jiacong Li / Yujiao Yang / Fei Gao / Yu Zhang / Yu Feng / Shuang Wang / ...Authors: Jing Shi / Lu Wang / Aijia Wen / Fulin Wang / Yuqiong Zhang / Libing Yu / Fangfang Li / Yuanling Jin / Zhenzhen Feng / Jiacong Li / Yujiao Yang / Fei Gao / Yu Zhang / Yu Feng / Shuang Wang / Wei Zhao / Wei Lin / ![]() Abstract: Transcription activation is established through extensive protein-protein and protein-DNA interactions that allow an activator to engage and remodel RNA polymerase. SoxS, a global transcription ...Transcription activation is established through extensive protein-protein and protein-DNA interactions that allow an activator to engage and remodel RNA polymerase. SoxS, a global transcription activator, diversely regulates subsets of stress response genes with different promoters, but the detailed SoxS-dependent transcription initiation mechanisms remain obscure. Here, we report cryo-EM structures of three SoxS-dependent transcription activation complexes (SoxS-TACI, SoxS-TACII and SoxS-TACIII) comprising of Escherichia coli RNA polymerase (RNAP), SoxS protein and three representative classes of SoxS-regulated promoters. The structures reveal that SoxS monomer orchestrates transcription initiation through specific interactions with the promoter DNA and different conserved domains of RNAP. In particular, SoxS is positioned in the opposite orientation in SoxS-TACIII to that in SoxS-TACI and SoxS-TACII, unveiling a novel mode of transcription activation. Strikingly, two universally conserved C-terminal domains of alpha subunit (αCTD) of RNAP associate with each other, bridging SoxS and region 4 of σ70. We show that SoxS interacts with RNAP directly and independently from DNA, remodeling the enzyme to activate transcription from cognate SoxS promoters while repressing transcription from UP-element containing promoters. Our data provide a comprehensive summary of SoxS-dependent promoter architectures and offer new insights into the αCTD contribution to transcription control in bacteria. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 758.6 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 613.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 32323MC ![]() 7w5wC ![]() 7w5yC M: map data used to model this data C: citing same article ( |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
-
Assembly
Deposited unit | ![]()
|
---|---|
1 |
|
-
Components
-Zwf promoter DNA ... , 2 types, 2 molecules 12
#1: DNA chain | Mass: 23298.924 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() ![]() |
---|---|
#2: DNA chain | Mass: 23120.801 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() ![]() |
-DNA-directed RNA polymerase subunit ... , 4 types, 5 molecules CDEAB
#3: Protein | ![]() Mass: 150804.922 Da / Num. of mol.: 1 / Mutation: D516V Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Gene: rpoB, groN, nitB, rif, ron, stl, stv, tabD, b3987, JW3950 Production host: ![]() ![]() ![]() ![]() |
---|---|
#4: Protein | ![]() Mass: 155366.781 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() ![]() |
#5: Protein | ![]() Mass: 10249.547 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() ![]() |
#8: Protein | ![]() Mass: 36558.680 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() ![]() |
-Protein , 2 types, 2 molecules FK
#6: Protein | Mass: 70352.242 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() |
---|---|
#7: Protein | Mass: 12931.844 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: ![]() |
-
Sample preparation
Component |
| ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Source (natural) |
| ||||||||||||||||||||||||
Source (recombinant) | Organism: ![]() ![]() ![]() | ||||||||||||||||||||||||
Buffer solution | pH: 7.5 | ||||||||||||||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied![]() ![]() | ||||||||||||||||||||||||
Vitrification![]() | Cryogen name: ETHANE |
-
Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
---|---|
Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source![]() ![]() |
Electron lens | Mode: BRIGHT FIELD![]() |
Image recording | Electron dose: 52 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-
Processing
CTF correction![]() | Type: NONE |
---|---|
3D reconstruction![]() | Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 116760 / Symmetry type: POINT |