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Yorodumi- EMDB-35131: Clostridium thermocellum RNA polymerase transcription open comple... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-35131 | |||||||||
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Title | Clostridium thermocellum RNA polymerase transcription open complex with SigI6 and its promoter | |||||||||
Map data | ||||||||||
Sample |
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Keywords | TRANSCRIPTION OPEN COMPLEX / SIGI / TRANSCRIPTION | |||||||||
Biological species | Acetivibrio thermocellus DSM 1313 (bacteria) / Acetivibrio thermocellus (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.36 Å | |||||||||
Authors | Li J / Zhang H / Li D / Feng Y / Zhu P | |||||||||
Funding support | China, 1 items
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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
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_35131.map.gz | 78.2 MB | EMDB map data format | |
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Header (meta data) | emd-35131-v30.xml emd-35131.xml | 24.4 KB 24.4 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_35131_fsc.xml | 10 KB | Display | FSC data file |
Images | emd_35131.png | 109.6 KB | ||
Masks | emd_35131_msk_1.map | 83.7 MB | Mask map | |
Filedesc metadata | emd-35131.cif.gz | 8.3 KB | ||
Others | emd_35131_half_map_1.map.gz emd_35131_half_map_2.map.gz | 65.4 MB 65.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-35131 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-35131 | HTTPS FTP |
-Validation report
Summary document | emd_35131_validation.pdf.gz | 949.1 KB | Display | EMDB validaton report |
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Full document | emd_35131_full_validation.pdf.gz | 948.7 KB | Display | |
Data in XML | emd_35131_validation.xml.gz | 17.4 KB | Display | |
Data in CIF | emd_35131_validation.cif.gz | 22.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-35131 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-35131 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_35131.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 1.04 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_35131_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_35131_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_35131_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Clostridium thermocellum RNA polymerase transcription open comple...
+Supramolecule #1: Clostridium thermocellum RNA polymerase transcription open comple...
+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 SigI6
+Macromolecule #6: DNA (80-mer)
+Macromolecule #7: DNA (80-mer)
+Macromolecule #8: ZINC ION
+Macromolecule #9: MAGNESIUM ION
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 13.09 mg/mL |
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Buffer | 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 |
Vitrification | Cryogen name: ETHANE |
Details | This sample was monodisperse. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Temperature | Min: 77.0 K / Max: 77.0 K |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Dimensions - Width: 3838 pixel / Digitization - Dimensions - Height: 3710 pixel / Digitization - Frames/image: 1-32 / Average exposure time: 0.25 sec. / Average electron dose: 1.875 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 70.0 µm / Calibrated defocus max: 2.5 µm / Calibrated defocus min: 1.5 µm / Calibrated magnification: 22500 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 22500 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |