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Yorodumi- EMDB-21920: Cryo-EM structure of Bacillus subtilis RNA Polymerase elongation ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-21920 | |||||||||
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Title | Cryo-EM structure of Bacillus subtilis RNA Polymerase elongation complex | |||||||||
Map data | Bacillus subtilis RNAP Elongation Complex | |||||||||
Sample |
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Keywords | DNA-DEPENDENT RNA POLYMERASE / TRANSCRIPTION / TRANSCRIPTION-DNA-RNA COMPLEX | |||||||||
Function / homology | Function and homology information DNA-directed RNA polymerase complex / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / protein dimerization activity / response to antibiotic / DNA-templated transcription / magnesium ion binding / DNA binding / zinc ion binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Bacillus subtilis (bacteria) / Escherichia coli BL21(DE3) (bacteria) / Bacillus subtilis (strain 168) (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.36 Å | |||||||||
Authors | Newing T / Tolun G | |||||||||
Citation | Journal: Nat Commun / Year: 2020 Title: Molecular basis for RNA polymerase-dependent transcription complex recycling by the helicase-like motor protein HelD. Authors: Timothy P Newing / Aaron J Oakley / Michael Miller / Catherine J Dawson / Simon H J Brown / James C Bouwer / Gökhan Tolun / Peter J Lewis / Abstract: In bacteria, transcription complexes stalled on DNA represent a major source of roadblocks for the DNA replication machinery that must be removed in order to prevent damaging collisions. Gram- ...In bacteria, transcription complexes stalled on DNA represent a major source of roadblocks for the DNA replication machinery that must be removed in order to prevent damaging collisions. Gram-positive bacteria contain a transcription factor HelD that is able to remove and recycle stalled complexes, but it was not known how it performed this function. Here, using single particle cryo-electron microscopy, we have determined the structures of Bacillus subtilis RNA polymerase (RNAP) elongation and HelD complexes, enabling analysis of the conformational changes that occur in RNAP driven by HelD interaction. HelD has a 2-armed structure which penetrates deep into the primary and secondary channels of RNA polymerase. One arm removes nucleic acids from the active site, and the other induces a large conformational change in the primary channel leading to removal and recycling of the stalled polymerase, representing a novel mechanism for recycling transcription complexes in bacteria. | |||||||||
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_21920.map.gz | 18.8 MB | EMDB map data format | |
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Header (meta data) | emd-21920-v30.xml emd-21920.xml | 25.1 KB 25.1 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_21920_fsc.xml | 10.3 KB | Display | FSC data file |
Images | emd_21920.png | 46.3 KB | ||
Filedesc metadata | emd-21920.cif.gz | 8.8 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-21920 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-21920 | HTTPS FTP |
-Validation report
Summary document | emd_21920_validation.pdf.gz | 535.5 KB | Display | EMDB validaton report |
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Full document | emd_21920_full_validation.pdf.gz | 535 KB | Display | |
Data in XML | emd_21920_validation.xml.gz | 9.7 KB | Display | |
Data in CIF | emd_21920_validation.cif.gz | 13.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-21920 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-21920 | HTTPS FTP |
-Related structure data
Related structure data | 6wvjMC 6wvkC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | |
EM raw data | EMPIAR-11051 (Title: Cryo-EM structure of Bacillus subtilis RNA Polymerase elongation complex Data size: 2.3 TB Data #1: Cryo-EM structure of Bacillus subtilis RNA Polymerase elongation complex [micrographs - multiframe]) |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_21920.map.gz / Format: CCP4 / Size: 20.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Bacillus subtilis RNAP Elongation Complex | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.84 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
+Entire : DNA-directed RNA polymerase elongation complex
+Supramolecule #1: DNA-directed RNA polymerase elongation complex
+Supramolecule #2: DNA-directed RNA polymerase subunit alpha, DNA-directed RNA polym...
+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: DNA (5'-D(*TP*GP*TP*CP*GP*GP*GP*CP*GP*TP*CP*CP*GP*CP*GP*CP*GP*CP*...
+Macromolecule #7: DNA (5'-D(P*AP*CP*GP*CP*CP*CP*GP*AP*CP*A)-3')
+Macromolecule #6: RNA (5'-R(P*GP*GP*CP*GP*CP*GP*CP*G)-3')
+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 | 2.50 mg/mL | ||||||||||||||||||
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Buffer | pH: 7.8 Component:
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Grid | Model: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY / Support film - Film thickness: 50 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 32 sec. / Pretreatment - Atmosphere: AIR | ||||||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV Details: Sample loading volume ranged between 2 and 3 microlitres. Samples were blotted for 5 seconds prior to vitrification.. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Name: GIF Quantum LS |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3838 pixel / Digitization - Dimensions - Height: 3710 pixel / Digitization - Frames/image: 1-40 / Number grids imaged: 2 / Number real images: 5185 / Average exposure time: 9.0 sec. / Average electron dose: 52.2 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 59500 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.8000000000000003 µm / Nominal defocus min: 0.6 µm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Space: REAL |
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Output model | PDB-6wvj: |