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Yorodumi- EMDB-33470: Cryo-EM structure of sigma70 bound HK022 putRNA-associated E.coli... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-33470 | ||||||||||||||||||
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Title | Cryo-EM structure of sigma70 bound HK022 putRNA-associated E.coli RNA polymerase elongation complex | ||||||||||||||||||
Map data | local-filtered map after post-process | ||||||||||||||||||
Sample |
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Keywords | transcription / RNA polymerase / anti-pausing / anti-termination / cryo-EM / HK022 put | ||||||||||||||||||
Function / homology | Function and homology information sigma factor antagonist complex / RNA polymerase complex / submerged biofilm formation / cellular response to cell envelope stress / bacterial-type RNA polymerase core enzyme binding / cytosolic DNA-directed RNA polymerase complex / regulation of DNA-templated transcription initiation / sigma factor activity / bacterial-type flagellum assembly / bacterial-type flagellum-dependent cell motility ...sigma factor antagonist complex / RNA polymerase complex / submerged biofilm formation / cellular response to cell envelope stress / bacterial-type RNA polymerase core enzyme binding / cytosolic DNA-directed RNA polymerase complex / regulation of DNA-templated transcription initiation / sigma factor activity / bacterial-type flagellum assembly / bacterial-type flagellum-dependent cell motility / nitrate assimilation / transcription elongation factor complex / regulation of DNA-templated transcription elongation / DNA-templated transcription initiation / transcription antitermination / cell motility / 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 / magnesium ion binding / DNA binding / zinc ion binding / membrane / cytosol / cytoplasm Similarity search - Function | ||||||||||||||||||
Biological species | Escherichia coli (strain K12) (bacteria) / Escherichia coli K-12 (bacteria) / Shamshuipovirus HK022 | ||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.61 Å | ||||||||||||||||||
Authors | Hwang S / Kang JY | ||||||||||||||||||
Funding support | Korea, Republic Of, United States, 5 items
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Citation | Journal: Nat Commun / Year: 2022 Title: Structural basis of transcriptional regulation by a nascent RNA element, HK022 putRNA. Authors: Seungha Hwang / Paul Dominic B Olinares / Jimin Lee / Jinwoo Kim / Brian T Chait / Rodney A King / Jin Young Kang / Abstract: Transcription, in which RNA polymerases (RNAPs) produce RNA from DNA, is the first step of gene expression. As such, it is highly regulated either by trans-elements like protein factors and/or by cis- ...Transcription, in which RNA polymerases (RNAPs) produce RNA from DNA, is the first step of gene expression. As such, it is highly regulated either by trans-elements like protein factors and/or by cis-elements like specific sequences on the DNA. Lambdoid phage HK022 contains a cis-element, put, which suppresses pausing and termination during transcription of the early phage genes. The putRNA transcript solely performs the anti-pausing/termination activities by interacting directly with the E.coli RNAP elongation complex (EC) by an unknown structural mechanism. In this study, we reconstituted putRNA-associated ECs and determined the structures using cryo-electron microscopy. The determined structures of putRNA-associated EC, putRNA-absent EC, and σ-bound EC suggest that the putRNA interaction with the EC counteracts swiveling, a conformational change previously identified to promote pausing and σ might modulate putRNA folding via σ-dependent pausing during elongation. | ||||||||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_33470.map.gz | 3.2 MB | EMDB map data format | |
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Header (meta data) | emd-33470-v30.xml emd-33470.xml | 27.8 KB 27.8 KB | Display Display | EMDB header |
Images | emd_33470.png | 41.4 KB | ||
Filedesc metadata | emd-33470.cif.gz | 9.6 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-33470 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-33470 | HTTPS FTP |
-Validation report
Summary document | emd_33470_validation.pdf.gz | 369.1 KB | Display | EMDB validaton report |
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Full document | emd_33470_full_validation.pdf.gz | 368.7 KB | Display | |
Data in XML | emd_33470_validation.xml.gz | 6.4 KB | Display | |
Data in CIF | emd_33470_validation.cif.gz | 7.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-33470 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-33470 | HTTPS FTP |
-Related structure data
Related structure data | 7xuiMC 7xueC 7xugC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_33470.map.gz / Format: CCP4 / Size: 98.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | local-filtered map after post-process | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.06 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Sample components
+Entire : sigma70 bound HK022 putRNA-associated E.coli RNA polymerase elong...
+Supramolecule #1: sigma70 bound HK022 putRNA-associated E.coli RNA polymerase elong...
+Supramolecule #2: RNA polymerase
+Supramolecule #3: DNA/RNA
+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 RpoD
+Macromolecule #6: template DNA
+Macromolecule #7: RNA (122-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 | 4 mg/mL | |||||||||||||||
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Buffer | pH: 8 Component:
Details: pH adjustment at 4'C | |||||||||||||||
Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 25 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.026000000000000002 kPa | |||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295 K / Instrument: FEI VITROBOT MARK IV / Details: using two layers of blot papers. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 8175 / Average electron dose: 42.16 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 70.0 µm / Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.6 µm / Nominal defocus min: 0.8 µm |
Sample stage | Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |