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Yorodumi- PDB-8i23: Clostridium thermocellum RNA polymerase transcription open comple... -
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-Basic information
Entry | Database: PDB / ID: 8i23 | ||||||
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Title | Clostridium thermocellum RNA polymerase transcription open complex with SigI1 and its promoter | ||||||
Components |
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Keywords | TRANSCRIPTION/DNA / TRANSCRIPTION OPEN COMPLEX / SIGI / TRANSCRIPTION / TRANSCRIPTION-DNA complex | ||||||
Function / homology | DNA / DNA (> 10) Function and homology information | ||||||
Biological species | Acetivibrio thermocellus DSM1313 (bacteria) Acetivibrio thermocellus DSM 1313 (bacteria) Acetivibrio thermocellus (bacteria) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / negative staining / cryo EM / Resolution: 3.03 Å | ||||||
Authors | Li, J. / Zhang, H. / Li, D. / Feng, Y. / Zhu, P. | ||||||
Funding support | China, 1items
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Citation | Journal: Nat Commun / Year: 2023 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. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8i23.cif.gz | 593.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8i23.ent.gz | 471.6 KB | Display | PDB format |
PDBx/mmJSON format | 8i23.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8i23_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 8i23_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 8i23_validation.xml.gz | 91 KB | Display | |
Data in CIF | 8i23_validation.cif.gz | 139.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i2/8i23 ftp://data.pdbj.org/pub/pdb/validation_reports/i2/8i23 | HTTPS FTP |
-Related structure data
Related structure data | 35130MC 8i24C M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-DNA-directed RNA polymerase subunit ... , 4 types, 5 molecules ABCDE
#1: Protein | Mass: 35071.125 Da / Num. of mol.: 2 / Mutation: 0 / Source method: isolated from a natural source Source: (natural) Acetivibrio thermocellus DSM 1313 (bacteria) 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) Acetivibrio thermocellus DSM1313 (bacteria) 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) Acetivibrio thermocellus DSM 1313 (bacteria) 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) Acetivibrio thermocellus DSM1313 (bacteria) Strain: DSM1313 / References: DNA-directed RNA polymerase |
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-Protein , 1 types, 1 molecules F
#5: Protein | Mass: 30714.949 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Acetivibrio thermocellus DSM1313 (bacteria) Strain: DSM1313 / Production host: Escherichia coli BL21(DE3) (bacteria) |
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-DNA chain , 2 types, 2 molecules OP
#6: DNA chain | Mass: 24897.059 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Acetivibrio thermocellus (bacteria) |
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#7: DNA chain | Mass: 24401.629 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Acetivibrio thermocellus (bacteria) |
-Non-polymers , 2 types, 3 molecules
#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 |
-Sample preparation
Component | Name: Clostridium thermocellum RNA polymerase transcription open complex with SigI1 its promoter Type: COMPLEX / Entity ID: #1-#7 / Source: MULTIPLE SOURCES | |||||||||||||||||||||||||
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Molecular weight |
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Source (natural) | Organism: Acetivibrio thermocellus DSM 1313 (bacteria) | |||||||||||||||||||||||||
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.: 23.54 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: YES / Vitrification applied: YES / Details: This sample was monodisperse. | |||||||||||||||||||||||||
EM staining | Type: NEGATIVE / Material: Uranyl Acetate | |||||||||||||||||||||||||
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 / 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 |
-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: 3.03 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 150741 / Algorithm: BACK PROJECTION / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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