+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-40874 | |||||||||
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Title | Cyanobacterial RNAP-EC | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Transcription regulation RNAP NusG cryo-EM / TRANSCRIPTION | |||||||||
Function / homology | Function and homology information transcription elongation-coupled chromatin remodeling / DNA-directed RNA polymerase complex / regulation of DNA-templated transcription elongation / transcription antitermination / DNA-templated transcription termination / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / protein dimerization activity / DNA-templated transcription ...transcription elongation-coupled chromatin remodeling / DNA-directed RNA polymerase complex / regulation of DNA-templated transcription elongation / transcription antitermination / DNA-templated transcription termination / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / protein dimerization activity / DNA-templated transcription / magnesium ion binding / DNA binding / zinc ion binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Synechococcus elongatus (bacteria) / synthetic construct (others) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.94 Å | |||||||||
Authors | Qayyum MZ / Imashimizu M / Leanca M / Vishwakarma RK / Bradley Riaz A / Yuzenkova Y / Murakami KS | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Proc Natl Acad Sci U S A / Year: 2024 Title: Structure and function of the Si3 insertion integrated into the trigger loop/helix of cyanobacterial RNA polymerase. Authors: M Zuhaib Qayyum / Masahiko Imashimizu / Miron Leanca / Rishi K Vishwakarma / Amber Riaz-Bradley / Yulia Yuzenkova / Katsuhiko S Murakami / Abstract: Cyanobacteria and evolutionarily related chloroplasts of algae and plants possess unique RNA polymerases (RNAPs) with characteristics that distinguish them from canonical bacterial RNAPs. The largest ...Cyanobacteria and evolutionarily related chloroplasts of algae and plants possess unique RNA polymerases (RNAPs) with characteristics that distinguish them from canonical bacterial RNAPs. The largest subunit of cyanobacterial RNAP (cyRNAP) is divided into two polypeptides, β'1 and β'2, and contains the largest known lineage-specific insertion domain, Si3, located in the middle of the trigger loop and spanning approximately half of the β'2 subunit. In this study, we present the X-ray crystal structure of Si3 and the cryo-EM structures of the cyRNAP transcription elongation complex plus the NusG factor with and without incoming nucleoside triphosphate (iNTP) bound at the active site. Si3 has a well-ordered and elongated shape that exceeds the length of the main body of cyRNAP, fits into cavities of cyRNAP in the absence of iNTP bound at the active site and shields the binding site of secondary channel-binding proteins such as Gre and DksA. A small transition from the trigger loop to the trigger helix upon iNTP binding results in a large swing motion of Si3; however, this transition does not affect the catalytic activity of cyRNAP due to its minimal contact with cyRNAP, NusG, or DNA. This study provides a structural framework for understanding the evolutionary significance of these features unique to cyRNAP and chloroplast RNAP and may provide insights into the molecular mechanism of transcription in specific environment of photosynthetic organisms and organelle. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_40874.map.gz | 122.4 MB | EMDB map data format | |
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Header (meta data) | emd-40874-v30.xml emd-40874.xml | 25.9 KB 25.9 KB | Display Display | EMDB header |
Images | emd_40874.png | 156.2 KB | ||
Filedesc metadata | emd-40874.cif.gz | 8.6 KB | ||
Others | emd_40874_half_map_1.map.gz emd_40874_half_map_2.map.gz | 226.3 MB 226.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-40874 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-40874 | HTTPS FTP |
-Validation report
Summary document | emd_40874_validation.pdf.gz | 858.6 KB | Display | EMDB validaton report |
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Full document | emd_40874_full_validation.pdf.gz | 858.2 KB | Display | |
Data in XML | emd_40874_validation.xml.gz | 16.2 KB | Display | |
Data in CIF | emd_40874_validation.cif.gz | 19 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-40874 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-40874 | HTTPS FTP |
-Related structure data
Related structure data | 8syiMC 8embC 8urwC 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_40874.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.87 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_40874_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_40874_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : CyRNAP-Elongation Complex
+Supramolecule #1: CyRNAP-Elongation Complex
+Macromolecule #1: DNA-directed RNA polymerase subunit alpha
+Macromolecule #2: DNA-directed RNA polymerase subunit beta
+Macromolecule #3: DNA-directed RNA polymerase subunit gamma
+Macromolecule #4: DNA-directed RNA polymerase subunit beta'
+Macromolecule #5: DNA-directed RNA polymerase subunit omega
+Macromolecule #6: Transcription termination/antitermination protein NusG
+Macromolecule #7: DNA (37-MER)
+Macromolecule #9: DNA (37-MER)
+Macromolecule #8: RNA (5'-R(P*UP*UP*CP*AP*AP*AP*GP*CP*GP*GP*AP*GP*AP*GP*GP*UP*A)-3')
+Macromolecule #10: MAGNESIUM ION
+Macromolecule #11: ZINC ION
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 / Details: 40mM Tris-HCl 200mM KCl 1mM EDTA 1mM DTT |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 45.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: OTHER / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.75 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: PDB ENTRY PDB model - PDB ID: |
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Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.94 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 176309 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |