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Yorodumi- EMDB-0700: cryo-EM structure of Escherichia coli Crl transcription activatio... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-0700 | |||||||||
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Title | cryo-EM structure of Escherichia coli Crl transcription activation complex | |||||||||
Map data | ||||||||||
Sample |
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Keywords | RNA polymerase / Escherichia coli / Crl / transcription activation / transcription initiation / transcription regulator / sigma S / TRANSCRIPTION | |||||||||
Function / homology | Function and homology information bacterial-type RNA polymerase core enzyme binding / sigma factor antagonist complex / RNA polymerase complex / submerged biofilm formation / cellular response to cell envelope stress / cytosolic DNA-directed RNA polymerase complex / regulation of DNA-templated transcription initiation / bacterial-type flagellum assembly / sigma factor activity / bacterial-type flagellum-dependent cell motility ...bacterial-type RNA polymerase core enzyme binding / sigma factor antagonist complex / RNA polymerase complex / submerged biofilm formation / cellular response to cell envelope stress / cytosolic DNA-directed RNA polymerase complex / regulation of DNA-templated transcription initiation / bacterial-type flagellum assembly / sigma factor activity / bacterial-type flagellum-dependent cell motility / nitrate assimilation / transcription elongation factor complex / regulation of DNA-templated transcription elongation / transcription antitermination / cell motility / DNA-templated transcription initiation / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / response to heat / protein-containing complex assembly / intracellular iron ion homeostasis / protein dimerization activity / response to antibiotic / negative regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / magnesium ion binding / DNA binding / zinc ion binding / membrane / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Escherichia coli K-12 (bacteria) / Escherichia coli (strain K12) (bacteria) / Escherichia coli (strain ATCC 8739 / DSM 1576 / Crooks) (bacteria) / synthetic construct (others) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.8 Å | |||||||||
Authors | Xu J / Zhang Y | |||||||||
Funding support | China, 2 items
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Citation | Journal: Elife / Year: 2019 Title: Crl activates transcription by stabilizing active conformation of the master stress transcription initiation factor. Authors: Juncao Xu / Kaijie Cui / Liqiang Shen / Jing Shi / Lingting Li / Linlin You / Chengli Fang / Guoping Zhao / Yu Feng / Bei Yang / Yu Zhang / Abstract: σ is a master transcription initiation factor that protects bacterial cells from various harmful environmental stresses including antibiotic pressure. Although its mechanism remains unclear, it is ...σ is a master transcription initiation factor that protects bacterial cells from various harmful environmental stresses including antibiotic pressure. Although its mechanism remains unclear, it is known that full activation of σ-mediated transcription requires a σ-specific activator, Crl. In this study, we determined a 3.80 Å cryo-EM structure of an transcription activation complex ( Crl-TAC) comprising σ-RNA polymerase (σ-RNAP) holoenzyme, Crl, and a nucleic-acid scaffold. The structure reveals that Crl interacts with domain 2 of σ (σ) and the RNAP core enzyme, but does not contact promoter DNA. Results from subsequent hydrogen-deuterium exchange mass spectrometry (HDX-MS) indicate that Crl stabilizes key structural motifs within σ to promote the assembly of the σ-RNAP holoenzyme and also to facilitate formation of an RNA polymerase-promoter DNA open complex (RPo). Our study demonstrates a unique DNA contact-independent mechanism of transcription activation, thereby defining a previously unrecognized mode of transcription activation in cells. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_0700.map.gz | 6.1 MB | EMDB map data format | |
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Header (meta data) | emd-0700-v30.xml emd-0700.xml | 31.1 KB 31.1 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_0700_fsc.xml | 8.6 KB | Display | FSC data file |
Images | emd_0700.png | 92.5 KB | ||
Filedesc metadata | emd-0700.cif.gz | 9.4 KB | ||
Others | emd_0700_half_map_1.map.gz emd_0700_half_map_2.map.gz | 40.8 MB 40.8 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-0700 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-0700 | HTTPS FTP |
-Related structure data
Related structure data | 6kj6MC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_0700.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 1.014 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Half map: #2
File | emd_0700_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_0700_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Escherichia coli Crl transcription activation complex(Crl-TAC)
+Supramolecule #1: Escherichia coli Crl transcription activation complex(Crl-TAC)
+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 RpoS
+Macromolecule #9: Sigma factor-binding protein Crl
+Macromolecule #6: DNA (51-MER)
+Macromolecule #7: DNA (51-MER)
+Macromolecule #8: RNA (5'-R(*CP*UP*CP*GP*A)-3')
+Macromolecule #10: ZINC ION
+Macromolecule #11: MAGNESIUM ION
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 12 mg/mL | |||||||||||||||
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Buffer | pH: 7.5 Component:
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Grid | Model: C-flat-1.2/1.3 4C / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 120 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 120 sec. / Pretreatment - Atmosphere: OTHER | |||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 283 K / Instrument: FEI VITROBOT MARK IV / Details: blot for 8 seconds before plunging. | |||||||||||||||
Details | This sample was monodisperse |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.6 µm / Nominal defocus min: 2.0 µm |
Sample stage | Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Number grids imaged: 1 / Number real images: 3290 / Average exposure time: 8.0 sec. / Average electron dose: 1.675 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |