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- PDB-8i24: Clostridium thermocellum RNA polymerase transcription open comple... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8i24 | ||||||
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Title | Clostridium thermocellum RNA polymerase transcription open complex with SigI6 and its promoter | ||||||
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![]() | TRANSCRIPTION / TRANSCRIPTION OPEN COMPLEX / SIGI | ||||||
Function / homology | DNA / DNA (> 10)![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.36 Å | ||||||
![]() | Li, J. / Zhang, H. / Li, D. / Feng, Y. / Zhu, P. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structure of the transcription open complex of distinct σ factors. Authors: Jie Li / Haonan Zhang / Dongyu Li / Ya-Jun Liu / Edward A Bayer / Qiu Cui / Yingang Feng / Ping Zhu / ![]() ![]() Abstract: Bacterial σ factors of the σ-family are widespread in Bacilli and Clostridia and are involved in the heat shock response, iron metabolism, virulence, and carbohydrate sensing. A multiplicity of σ ...Bacterial σ factors of the σ-family are widespread in Bacilli and Clostridia and are involved in the heat shock response, iron metabolism, virulence, and carbohydrate sensing. A multiplicity of σ paralogues in some cellulolytic bacteria have been shown to be responsible for the regulation of the cellulosome, a multienzyme complex that mediates efficient cellulose degradation. Here, we report two structures at 3.0 Å and 3.3 Å of two transcription open complexes formed by two σ factors, SigI1 and SigI6, respectively, from the thermophilic, cellulolytic bacterium, Clostridium thermocellum. These structures reveal a unique, hitherto-unknown recognition mode of bacterial transcriptional promoters, both with respect to domain organization and binding to promoter DNA. The key characteristics that determine the specificities of the σ paralogues were further revealed by comparison of the two structures. Consequently, the σ factors represent a distinct set of the σ-family σ factors, thus highlighting the diversity of bacterial transcription. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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PDBx/mmCIF format | ![]() | 594.9 KB | Display | ![]() |
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PDB format | ![]() | 473.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 1.3 MB | Display | ![]() |
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Full document | ![]() | 1.3 MB | Display | |
Data in XML | ![]() | 90.3 KB | Display | |
Data in CIF | ![]() | 137.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 35131MC ![]() 8i23C C: citing same article ( M: map data used to model this data |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Components
-DNA-directed RNA polymerase subunit ... , 4 types, 5 molecules BACDE
#1: Protein | Mass: 35071.125 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() Strain: DSM1313 / References: DNA-directed RNA polymerase #2: Protein | | Mass: 140110.359 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: DSM1313 / References: DNA-directed RNA polymerase #3: Protein | | Mass: 132698.844 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: DSM1313 / References: DNA-directed RNA polymerase #4: Protein | | Mass: 8783.143 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: DSM1313 / References: DNA-directed RNA polymerase |
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-Protein , 1 types, 1 molecules F
#5: Protein | Mass: 30092.365 Da / Num. of mol.: 1 / Mutation: C167S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: DSM1313 / Production host: ![]() ![]() |
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-DNA chain , 2 types, 2 molecules OP
#6: DNA chain | Mass: 24794.967 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() |
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#7: DNA chain | Mass: 24606.746 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() |
-Non-polymers , 2 types, 3 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/MG.gif)
#8: Chemical | #9: Chemical | ChemComp-MG / | |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: Clostridium thermocellum RNA polymerase transcription open complex with SigI6 and its promoter Type: COMPLEX / Entity ID: #1-#7 / Source: MULTIPLE SOURCES | ||||||||||||||||
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Molecular weight |
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Source (natural) | Organism: ![]() | ||||||||||||||||
Buffer solution | pH: 8 Details: 20 mM Tris-HCl pH 8.0, 150 mM NaCl, 2 mM DTT, 0.2 mM EDTA, 5% (v/v) glycerol, 10 mM MgCl2 | ||||||||||||||||
Specimen | Conc.: 13.09 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: This sample was monodisperse. | ||||||||||||||||
Vitrification | Cryogen name: ETHANE |
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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: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 22500 X / Calibrated magnification: 22500 X / Nominal defocus max: 2500 nm / Nominal defocus min: 1500 nm / Calibrated defocus min: 1500 nm / Calibrated defocus max: 2500 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: BASIC |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (max): 77 K / Temperature (min): 77 K |
Image recording | Average exposure time: 0.25 sec. / Electron dose: 1.875 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
Image scans | Width: 3838 / Height: 3710 / Movie frames/image: 32 / Used frames/image: 1-32 |
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Processing
Software | Name: PHENIX / Version: 1.19.2_4158: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.36 Å / Resolution method: OTHER / Num. of particles: 22500 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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