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Yorodumi- EMDB-74515: E. coli RNA polymerase elongation complex containing the unnatura... -
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Open data
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Basic information
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| Title | E. coli RNA polymerase elongation complex containing the unnatural dP:Z*TP base pair in a trigger-loop-closed conformation | ||||||||||||||||||
Map data | E. coli RNA polymerase elongation complex containing the unnatural dP:Z*TP base pair in a trigger-loop-closed conformation. | ||||||||||||||||||
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Keywords | E. coli RNA polymerase elongation complex containing the unnatural dP:Z*TP base pair in a trigger-loop-closed conformation / TRANSCRIPTION / TRANSCRIPTION-DNA-RNA complex | ||||||||||||||||||
| Function / homology | Function and homology informationRNA polymerase complex / submerged biofilm formation / cellular response to cell envelope stress / regulation of DNA-templated transcription initiation / nitrate assimilation / cytosolic DNA-directed RNA polymerase complex / bacterial-type flagellum assembly / bacterial-type RNA polymerase core enzyme binding / bacterial-type flagellum-dependent cell motility / DNA-directed RNA polymerase complex ...RNA polymerase complex / submerged biofilm formation / cellular response to cell envelope stress / regulation of DNA-templated transcription initiation / nitrate assimilation / cytosolic DNA-directed RNA polymerase complex / bacterial-type flagellum assembly / bacterial-type RNA polymerase core enzyme binding / bacterial-type flagellum-dependent cell motility / DNA-directed RNA polymerase complex / cell motility / DNA-templated transcription elongation / regulation of DNA-templated transcription elongation / transcription antitermination / DNA-templated transcription initiation / ribonucleoside binding / DNA-directed RNA polymerase / DNA-directed RNA polymerase activity / response to heat / protein-containing complex assembly / intracellular iron ion homeostasis / protein dimerization activity / response to antibiotic / magnesium ion binding / DNA-templated transcription / DNA binding / zinc ion binding / membrane / cytosol / cytoplasm Similarity search - Function | ||||||||||||||||||
| Biological species | ![]() | ||||||||||||||||||
| Method | single particle reconstruction / cryo EM / Resolution: 2.75 Å | ||||||||||||||||||
Authors | Li Q / Benner SA / Wang D | ||||||||||||||||||
| Funding support | United States, 5 items
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Citation | Journal: Nat Commun / Year: 2026Title: Structural basis of transcription of the hachimoji eight-letter alphabet by E. coli RNA polymerase. Authors: Qingrong Li / Hyo-Joong Kim / Yan Liu / Juntaek Oh / Peini Hou / Shuichi Hoshika / Grigore Pintilie / Sriram Aiyer / Jenny Chong / Dmitry Lyumkis / Steven A Benner / Dong Wang / ![]() Abstract: Expanded genetic alphabets with synthetic nucleotides can greatly increase the chemical diversity of nucleic acids, enabling new molecular functions. Because cellular transcription is executed by ...Expanded genetic alphabets with synthetic nucleotides can greatly increase the chemical diversity of nucleic acids, enabling new molecular functions. Because cellular transcription is executed by multi-subunit RNA polymerases, the compatibility of unnatural base pairs with this machinery is essential for engineering expanded genetic systems. Here we demonstrate that Escherichia coli RNA polymerase efficiently transcribes an eight-letter genetic alphabet with two orthogonal unnatural base pairs: P:Z and B:S pairs. To overcome G:Z misincorporation, we synthesize a higher-fidelity analogue, termed Z*, in which the C5 nitro group is replaced with a carboxamide. To elucidate substrate-recognition mechanisms, we determine four cryo-electron microscopy structures of RNA polymerase incorporating dZ:PTP or dP:Z*TP at 2.42-2.75 Å resolution. These structures, together with our early work on S:B pair, show that E. coli RNA polymerase is able to efficiently recognize these unnatural base pairs in the same manner as natural base pairs. Collectively, these results establish the feasibility of an eight-letter genetic alphabet for transcription. | ||||||||||||||||||
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Structure visualization
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Downloads & links
-EMDB archive
| Map data | emd_74515.map.gz | 230.4 MB | EMDB map data format | |
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| Header (meta data) | emd-74515-v30.xml emd-74515.xml | 34 KB 34 KB | Display Display | EMDB header |
| FSC (resolution estimation) | emd_74515_fsc.xml | 13.2 KB | Display | FSC data file |
| Images | emd_74515.png | 54.1 KB | ||
| Filedesc metadata | emd-74515.cif.gz | 9.2 KB | ||
| Others | emd_74515_half_map_1.map.gz emd_74515_half_map_2.map.gz | 226.9 MB 226.9 MB | ||
| Archive directory | https://data.pdbj.org/pub/emdb/structures/EMD-74515 ftp://data.pdbj.org/pub/emdb/structures/EMD-74515 | HTTPS FTP |
-Related structure data
| Related structure data | ![]() 9zp3MC ![]() 9zp1C ![]() 9zp2C ![]() 9zp4C M: atomic model generated by this map C: citing same article ( |
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| Similar structure data | Similarity search - Function & homology F&H Search |
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Links
| EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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| Related items in Molecule of the Month |
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Map
| File | Download / File: emd_74515.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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| Annotation | E. coli RNA polymerase elongation complex containing the unnatural dP:Z*TP base pair in a trigger-loop-closed conformation. | ||||||||||||||||||||||||||||||||||||
| Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
| Voxel size | X=Y=Z: 0.743 Å | ||||||||||||||||||||||||||||||||||||
| Density |
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| Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
| Details | EMDB XML:
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-Supplemental data
-Half map: E. coli RNA polymerase elongation complex containing the...
| File | emd_74515_half_map_1.map | ||||||||||||
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| Annotation | E. coli RNA polymerase elongation complex containing the unnatural dP:Z*TP base pair in a trigger-loop-closed conformation. | ||||||||||||
| Projections & Slices |
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| Density Histograms |
-Half map: E. coli RNA polymerase elongation complex containing the...
| File | emd_74515_half_map_2.map | ||||||||||||
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| Annotation | E. coli RNA polymerase elongation complex containing the unnatural dP:Z*TP base pair in a trigger-loop-closed conformation. | ||||||||||||
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| Density Histograms |
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Sample components
+Entire : E. coli RNA polymerase elongation complex containing the unnatura...
+Supramolecule #1: E. coli RNA polymerase elongation complex containing the unnatura...
+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: Non-template strand DNA
+Macromolecule #7: Template strand DNA
+Macromolecule #6: RNA
+Macromolecule #8: ZINC ION
+Macromolecule #9: [[(2~{R},3~{R},4~{R},5~{S})-5-(5-aminocarbonyl-6-azanyl-2-oxidany...
+Macromolecule #10: MAGNESIUM ION
+Macromolecule #11: water
-Experimental details
-Structure determination
| Method | cryo EM |
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Processing | single particle reconstruction |
| Aggregation state | particle |
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Sample preparation
| Buffer | pH: 7.5 |
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| Vitrification | Cryogen name: ETHANE |
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Electron microscopy
| Microscope | TFS KRIOS |
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| Image recording | Film or detector model: TFS FALCON 4i (4k x 4k) / Average electron dose: 30.0 e/Å2 |
| Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
| Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm |
| Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Keywords
Authors
United States, 5 items
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Processing
FIELD EMISSION GUN


