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Yorodumi- EMDB-72053: SARS-CoV-2 core polymerase complex bound to RNA, araUMP, and UTP -
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Open data
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Basic information
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| Title | SARS-CoV-2 core polymerase complex bound to RNA, araUMP, and UTP | |||||||||
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Keywords | RNA-dependent RNA polymerase (RdRp) / Viral RNA synthesis / arabinose UTP / Uridine triphosphate / nsp7 / nsp8 / nsp12 / VIRAL PROTEIN | |||||||||
| Function / homology | Function and homology informationprotein guanylyltransferase activity / RNA endonuclease activity producing 3'-phosphomonoesters, hydrolytic mechanism / 5'-3' RNA helicase activity / Lyases; Phosphorus-oxygen lyases / Assembly of the SARS-CoV-2 Replication-Transcription Complex (RTC) / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / Maturation of replicase proteins / TRAF3-dependent IRF activation pathway / ISG15-specific peptidase activity / Transcription of SARS-CoV-2 sgRNAs ...protein guanylyltransferase activity / RNA endonuclease activity producing 3'-phosphomonoesters, hydrolytic mechanism / 5'-3' RNA helicase activity / Lyases; Phosphorus-oxygen lyases / Assembly of the SARS-CoV-2 Replication-Transcription Complex (RTC) / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / Maturation of replicase proteins / TRAF3-dependent IRF activation pathway / ISG15-specific peptidase activity / Transcription of SARS-CoV-2 sgRNAs / snRNP Assembly / Translation of Replicase and Assembly of the Replication Transcription Complex / Replication of the SARS-CoV-2 genome / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / double membrane vesicle viral factory outer membrane / SARS coronavirus main proteinase / host cell endoplasmic reticulum-Golgi intermediate compartment / host cell endosome / 3'-5'-RNA exonuclease activity / symbiont-mediated degradation of host mRNA / 5'-3' DNA helicase activity / mRNA guanylyltransferase / symbiont-mediated suppression of host toll-like receptor signaling pathway / G-quadruplex RNA binding / symbiont-mediated suppression of host ISG15-protein conjugation / mRNA guanylyltransferase activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / DNA helicase / omega peptidase activity / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / symbiont-mediated suppression of host NF-kappaB cascade / SARS-CoV-2 modulates host translation machinery / symbiont-mediated perturbation of host ubiquitin-like protein modification / host cell Golgi apparatus / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / methyltransferase cap1 activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / ubiquitinyl hydrolase 1 / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / lyase activity / cysteine-type deubiquitinase activity / single-stranded RNA binding / viral protein processing / host cell perinuclear region of cytoplasm / host cell endoplasmic reticulum membrane / RNA helicase / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / symbiont-mediated suppression of host gene expression / copper ion binding / viral translational frameshifting / symbiont-mediated activation of host autophagy / RNA-directed RNA polymerase / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / lipid binding / host cell nucleus / SARS-CoV-2 activates/modulates innate and adaptive immune responses / ATP hydrolysis activity / proteolysis / DNA-templated transcription / RNA binding / zinc ion binding / ATP binding Similarity search - Function | |||||||||
| Biological species | ![]() | |||||||||
| Method | single particle reconstruction / cryo EM / Resolution: 3.1 Å | |||||||||
Authors | Xiao Z / Kirchdeorfer RN | |||||||||
| Funding support | United States, 2 items
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Citation | Journal: bioRxiv / Year: 2025 Title: The 2'-endo conformation of arabinose-CTP and arabinose-UTP inhibit viral polymerases by inducing long pauses. Authors: Ziyang Xiao / Arnab Das / Abha Jain / Thomas K Anderson / Craig E Cameron / Jamie J Arnold / David Dulin / Robert N Kirchdoerfer / ![]() Abstract: Key to supporting human health in the face of evolving viruses is the development of novel antiviral drug scaffolds with the potential for broad inhibition of viral families. Nucleoside analogs are a ...Key to supporting human health in the face of evolving viruses is the development of novel antiviral drug scaffolds with the potential for broad inhibition of viral families. Nucleoside analogs are a key class of drugs that have demonstrated potential for the inhibition of several viral species. Here, we evaluate arabinose nucleotides (ara-NTP) as inhibitors of the SARS-CoV-2 and poliovirus polymerases using biochemistry, biophysics and structural biology. Ara-NTPs compete poorly with their natural counterparts for incorporation into RNA by viral polymerases. However, upon incorporation, ara-NMPs induce long polymerase pausing in both SARS-CoV-2 and poliovirus polymerase RNA elongation. Our studies suggest that subsequent nucleotide incorporation is inhibited at the catalytic step due to the 2'-endo sugar pucker of the incorporated ara-NMP. | |||||||||
| History |
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Structure visualization
| Supplemental images |
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Downloads & links
-EMDB archive
| Map data | emd_72053.map.gz | 59.7 MB | EMDB map data format | |
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| Header (meta data) | emd-72053-v30.xml emd-72053.xml | 29.1 KB 29.1 KB | Display Display | EMDB header |
| FSC (resolution estimation) | emd_72053_fsc.xml | 8.4 KB | Display | FSC data file |
| Images | emd_72053.png | 57.7 KB | ||
| Masks | emd_72053_msk_1.map | 64 MB | Mask map | |
| Filedesc metadata | emd-72053.cif.gz | 8 KB | ||
| Others | emd_72053_half_map_1.map.gz emd_72053_half_map_2.map.gz | 59.4 MB 59.4 MB | ||
| Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-72053 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-72053 | HTTPS FTP |
-Related structure data
| Related structure data | ![]() 9pyzMC ![]() 9blfC ![]() 9pywC ![]() 9pz0C 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_72053.map.gz / Format: CCP4 / Size: 64 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: 1.064 Å | ||||||||||||||||||||||||||||||||||||
| Density |
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| Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
| Details | EMDB XML:
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-Supplemental data
-Mask #1
| File | emd_72053_msk_1.map | ||||||||||||
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| Density Histograms |
-Half map: #2
| File | emd_72053_half_map_1.map | ||||||||||||
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| Density Histograms |
-Half map: #1
| File | emd_72053_half_map_2.map | ||||||||||||
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| Density Histograms |
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Sample components
+Entire : SARS-CoV-2 core polymerase complex bound to RNA, araUMP, and UTP
+Supramolecule #1: SARS-CoV-2 core polymerase complex bound to RNA, araUMP, and UTP
+Supramolecule #2: nsp12 RNA-dependent RNA polymerase
+Supramolecule #3: Replication co-factors of RNA-dependent RNA polymerase
+Supramolecule #4: RNA
+Macromolecule #1: RNA-directed RNA polymerase nsp12
+Macromolecule #2: Non-structural protein 8
+Macromolecule #3: Non-structural protein 7
+Macromolecule #4: Primer RNA
+Macromolecule #5: Template RNA
+Macromolecule #6: MAGNESIUM ION
+Macromolecule #7: ZINC ION
+Macromolecule #8: URIDINE 5'-TRIPHOSPHATE
-Experimental details
-Structure determination
| Method | cryo EM |
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Processing | single particle reconstruction |
| Aggregation state | particle |
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Sample preparation
| Concentration | 8 mg/mL |
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| Buffer | pH: 8 |
| Grid | Model: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR |
| Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
| Microscope | FEI TALOS ARCTICA |
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| Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV |
| Software | Name: EPU (ver. 3.6.0.6389) |
| Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 4501 / Average exposure time: 4.52 sec. / Average electron dose: 55.0 e/Å2 |
| Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
| Electron optics | C2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm |
| Experimental equipment | ![]() Model: Talos Arctica / Image courtesy: FEI Company |
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Keywords
Authors
United States, 2 items
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Processing
FIELD EMISSION GUN

