+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-1577 | |||||||||
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Title | Bacillus subtilis RNA polymerase core | |||||||||
Map data | RNAP core from Bacillus subtilis | |||||||||
Sample |
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Keywords | RNA polymerase Ribonucleic acid synthesis Firmicutes | |||||||||
Biological species | Bacillus subtilis (bacteria) | |||||||||
Method | single particle reconstruction / negative staining / Resolution: 25.0 Å | |||||||||
Authors | Yang X / Molimau S / Doherty GP / Marles-Wright J / Rothnagel R / Hankamer B / Lewis RJ / Lewis PJ | |||||||||
Citation | Journal: EMBO Rep / Year: 2009 Title: The structure of bacterial RNA polymerase in complex with the essential transcription elongation factor NusA. Authors: Xiao Yang / Seeseei Molimau / Geoff P Doherty / Elecia B Johnston / Jon Marles-Wright / Rosalba Rothnagel / Ben Hankamer / Richard J Lewis / Peter J Lewis / Abstract: There are three stages of transcribing DNA into RNA. These stages are initiation, elongation and termination, and they are well-understood biochemically. However, despite the plethora of structural ...There are three stages of transcribing DNA into RNA. These stages are initiation, elongation and termination, and they are well-understood biochemically. However, despite the plethora of structural information made available on RNA polymerase in the last decade, little is available for RNA polymerase in complex with transcription elongation factors. To understand the mechanisms of transcriptional regulation, we describe the first structure, to our knowledge, for a bacterial RNA polymerase in complex with an essential transcription elongation factor. The resulting structure formed between the RNA polymerase and NusA from Bacillus subtilis provides important insights into the transition from an initiation complex to an elongation complex, and how NusA is able to modulate transcription elongation and termination. | |||||||||
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_1577.map.gz | 1.1 MB | EMDB map data format | |
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Header (meta data) | emd-1577-v30.xml emd-1577.xml | 8.2 KB 8.2 KB | Display Display | EMDB header |
Images | 1577.gif | 50.6 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-1577 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-1577 | HTTPS FTP |
-Validation report
Summary document | emd_1577_validation.pdf.gz | 229.1 KB | Display | EMDB validaton report |
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Full document | emd_1577_full_validation.pdf.gz | 228.2 KB | Display | |
Data in XML | emd_1577_validation.xml.gz | 5.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1577 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1577 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_1577.map.gz / Format: CCP4 / Size: 1.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | RNAP core from Bacillus subtilis | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 3.9 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 : Bacillus subtilis RNA polymerase core
Entire | Name: Bacillus subtilis RNA polymerase core |
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Components |
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-Supramolecule #1000: Bacillus subtilis RNA polymerase core
Supramolecule | Name: Bacillus subtilis RNA polymerase core / type: sample / ID: 1000 / Details: Monodisperse / Oligomeric state: Monomeric / Number unique components: 1 |
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Molecular weight | Experimental: 400 KDa / Theoretical: 400 KDa / Method: Gel filtration |
-Macromolecule #1: RNA polymerase
Macromolecule | Name: RNA polymerase / type: protein_or_peptide / ID: 1 / Name.synonym: RNA polymerase / Details: Obtained by negative staining / Number of copies: 1 / Oligomeric state: Monomer / Recombinant expression: No |
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Source (natural) | Organism: Bacillus subtilis (bacteria) / Strain: subtilis str. 168 / Tissue: Cytoplasm |
Molecular weight | Experimental: 400 KDa / Theoretical: 400 KDa |
-Experimental details
-Structure determination
Method | negative staining |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.8 Details: 20 mM Tris-HCl pH 7.8, 150 mM NaCl, 10 mM MgCl2, 5% (v/v) glycerol and 1 mM DTT |
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Staining | Type: NEGATIVE / Details: Negative stain with 1% uranyl acetate |
Grid | Details: Home made carbon |
Vitrification | Cryogen name: NONE / Instrument: OTHER |
-Electron microscopy
Microscope | FEI TECNAI F30 |
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Image recording | Digitization - Sampling interval: 3.9 µm / Number real images: 240 / Bits/pixel: 16 |
Electron beam | Acceleration voltage: 300 kV / Electron source: OTHER |
Electron optics | Illumination mode: OTHER / Imaging mode: OTHER |
Sample stage | Specimen holder: Eucentric / Specimen holder model: GATAN LIQUID NITROGEN |
Experimental equipment | Model: Tecnai F30 / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 25.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: EMAN / Number images used: 12622 |
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