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Yorodumi- EMDB-40707: SARS-CoV-2 replication-transcription complex bound to RNA-nsp9, a... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-40707 | |||||||||
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Title | SARS-CoV-2 replication-transcription complex bound to RNA-nsp9, as a noncatalytic RNA-nsp9 binding mode | |||||||||
Map data | Composite sharpened map | |||||||||
Sample |
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Keywords | RTC / nsp12 / nsp9 / NiRAN / SARS-CoV-2 / deRNAylation / mRNA capping / UMPCPP / VIRAL PROTEIN | |||||||||
Function / homology | Function and homology information protein guanylyltransferase activity / RNA endonuclease activity, producing 3'-phosphomonoesters / mRNA guanylyltransferase activity / 5'-3' RNA helicase activity / Lyases; Phosphorus-oxygen lyases / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / Assembly of the SARS-CoV-2 Replication-Transcription Complex (RTC) / Maturation of replicase proteins / ISG15-specific peptidase activity / Transcription of SARS-CoV-2 sgRNAs ...protein guanylyltransferase activity / RNA endonuclease activity, producing 3'-phosphomonoesters / mRNA guanylyltransferase activity / 5'-3' RNA helicase activity / Lyases; Phosphorus-oxygen lyases / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / Assembly of the SARS-CoV-2 Replication-Transcription Complex (RTC) / Maturation of replicase proteins / ISG15-specific peptidase activity / Transcription of SARS-CoV-2 sgRNAs / symbiont-mediated suppression of host NF-kappaB cascade / Translation of Replicase and Assembly of the Replication Transcription Complex / TRAF3-dependent IRF activation pathway / Replication of the SARS-CoV-2 genome / snRNP Assembly / double membrane vesicle viral factory outer membrane / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / 5'-3' DNA helicase activity / 3'-5'-RNA exonuclease activity / SARS coronavirus main proteinase / host cell endoplasmic reticulum-Golgi intermediate compartment / host cell endosome / symbiont-mediated suppression of host toll-like receptor signaling pathway / symbiont-mediated degradation of host mRNA / mRNA guanylyltransferase / symbiont-mediated suppression of host ISG15-protein conjugation / G-quadruplex RNA binding / omega peptidase activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / SARS-CoV-2 modulates host translation machinery / mRNA (guanine-N7)-methyltransferase / host cell Golgi apparatus / methyltransferase cap1 / symbiont-mediated perturbation of host ubiquitin-like protein modification / DNA helicase / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / single-stranded RNA binding / host cell perinuclear region of cytoplasm / viral protein processing / host cell endoplasmic reticulum membrane / lyase activity / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / RNA helicase / viral translational frameshifting / induction by virus of host autophagy / copper ion binding / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / DNA-templated transcription / lipid binding / host cell nucleus / SARS-CoV-2 activates/modulates innate and adaptive immune responses / ATP hydrolysis activity / proteolysis / RNA binding / zinc ion binding / ATP binding / membrane Similarity search - Function | |||||||||
Biological species | Severe acute respiratory syndrome coronavirus 2 / Severe acute respiratory syndrome coronavirus | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.06 Å | |||||||||
Authors | Small GI / Darst SA / Campbell EA | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Mol Cell / Year: 2023 Title: Structural and functional insights into the enzymatic plasticity of the SARS-CoV-2 NiRAN domain. Authors: Gabriel I Small / Olga Fedorova / Paul Dominic B Olinares / Joshua Chandanani / Anoosha Banerjee / Young Joo Choi / Henrik Molina / Brian T Chait / Seth A Darst / Elizabeth A Campbell / Abstract: The enzymatic activity of the SARS-CoV-2 nidovirus RdRp-associated nucleotidyltransferase (NiRAN) domain is essential for viral propagation, with three distinct activities associated with ...The enzymatic activity of the SARS-CoV-2 nidovirus RdRp-associated nucleotidyltransferase (NiRAN) domain is essential for viral propagation, with three distinct activities associated with modification of the nsp9 N terminus, NMPylation, RNAylation, and deRNAylation/capping via a GDP-polyribonucleotidyltransferase reaction. The latter two activities comprise an unconventional mechanism for initiating viral RNA 5' cap formation, while the role of NMPylation is unclear. The structural mechanisms for these diverse enzymatic activities have not been properly delineated. Here, we determine high-resolution cryoelectron microscopy (cryo-EM) structures of catalytic intermediates for the NMPylation and deRNAylation/capping reactions, revealing diverse nucleotide binding poses and divalent metal ion coordination sites to promote its repertoire of activities. The deRNAylation/capping structure explains why GDP is a preferred substrate for the capping reaction over GTP. Altogether, these findings enhance our understanding of the promiscuous coronaviral NiRAN domain, a therapeutic target, and provide an accurate structural platform for drug development. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_40707.map.gz | 58.4 MB | EMDB map data format | |
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Header (meta data) | emd-40707-v30.xml emd-40707.xml | 28.4 KB 28.4 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_40707_fsc.xml | 8.4 KB | Display | FSC data file |
Images | emd_40707.png | 44 KB | ||
Filedesc metadata | emd-40707.cif.gz | 7.2 KB | ||
Others | emd_40707_additional_1.map.gz emd_40707_additional_2.map.gz emd_40707_additional_3.map.gz emd_40707_half_map_1.map.gz emd_40707_half_map_2.map.gz | 14 MB 59.7 MB 59.6 MB 59.4 MB 59.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-40707 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-40707 | HTTPS FTP |
-Validation report
Summary document | emd_40707_validation.pdf.gz | 900.6 KB | Display | EMDB validaton report |
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Full document | emd_40707_full_validation.pdf.gz | 900.2 KB | Display | |
Data in XML | emd_40707_validation.xml.gz | 16.7 KB | Display | |
Data in CIF | emd_40707_validation.cif.gz | 21.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-40707 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-40707 | HTTPS FTP |
-Related structure data
Related structure data | 8sqjMC 8sq9C 8sqkC C: citing same article (ref.) M: atomic model generated by this map |
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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_40707.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | Composite sharpened map | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.0825 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: Composite locally filtered map
File | emd_40707_additional_1.map | ||||||||||||
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Annotation | Composite locally filtered map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Consensus map used in composite
File | emd_40707_additional_2.map | ||||||||||||
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Annotation | Consensus map used in composite | ||||||||||||
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Density Histograms |
-Additional map: Focused refinement map used in composite
File | emd_40707_additional_3.map | ||||||||||||
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Annotation | Focused refinement map used in composite | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Composite half map A
File | emd_40707_half_map_1.map | ||||||||||||
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Annotation | Composite half map A | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Composite half map B
File | emd_40707_half_map_2.map | ||||||||||||
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Annotation | Composite half map B | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : SARS-CoV-2 replication-transcription complex bound to RNA-nsp9, a...
+Supramolecule #1: SARS-CoV-2 replication-transcription complex bound to RNA-nsp9, a...
+Macromolecule #1: RNA-directed RNA polymerase
+Macromolecule #2: Non-structural protein 8
+Macromolecule #3: Non-structural protein 7
+Macromolecule #4: Non-structural protein 9
+Macromolecule #5: Primer RNA
+Macromolecule #6: Template RNA
+Macromolecule #7: SARS-CoV-2 5' UTR
+Macromolecule #8: 5'-O-[(R)-hydroxy(thiophosphonooxy)phosphoryl]guanosine
+Macromolecule #9: MAGNESIUM ION
+Macromolecule #10: ZINC ION
+Macromolecule #11: water
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | TFS KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 51.51 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: 1.8 µm / Nominal defocus min: 0.8 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |