+Open data
-Basic information
Entry | Database: PDB / ID: 8gwb | |||||||||
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Title | SARS-CoV-2 E-RTC complex with RNA-nsp9 | |||||||||
Components |
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Keywords | VIRAL PROTEIN / SARS-CoV-2 / capping / nucleotide analogue inhibitor / cryo-EM | |||||||||
Function / homology | Function and homology information viral genome replication / methyltransferase activity / 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 ...viral genome replication / methyltransferase activity / 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 / 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 / SARS coronavirus main proteinase / host cell endosome / host cell endoplasmic reticulum-Golgi intermediate compartment / 3'-5'-RNA exonuclease activity / 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 / SARS-CoV-2 modulates host translation machinery / omega peptidase activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / methylation / mRNA (guanine-N7)-methyltransferase / host cell Golgi apparatus / methyltransferase cap1 / symbiont-mediated perturbation of host ubiquitin-like protein modification / endonuclease activity / mRNA (nucleoside-2'-O-)-methyltransferase activity / DNA helicase / 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 endoplasmic reticulum membrane / host cell perinuclear region of cytoplasm / viral protein processing / lyase activity / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / RNA helicase / 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 | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.75 Å | |||||||||
Authors | Yan, L.M. / Rao, Z.H. / Lou, Z.Y. | |||||||||
Funding support | China, 2items
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Citation | Journal: Cell / Year: 2022 Title: A mechanism for SARS-CoV-2 RNA capping and its inhibition by nucleotide analog inhibitors. Authors: Liming Yan / Yucen Huang / Ji Ge / Zhenyu Liu / Pengchi Lu / Bo Huang / Shan Gao / Junbo Wang / Liping Tan / Sihan Ye / Fengxi Yu / Weiqi Lan / Shiya Xu / Feng Zhou / Lei Shi / Luke W Guddat ...Authors: Liming Yan / Yucen Huang / Ji Ge / Zhenyu Liu / Pengchi Lu / Bo Huang / Shan Gao / Junbo Wang / Liping Tan / Sihan Ye / Fengxi Yu / Weiqi Lan / Shiya Xu / Feng Zhou / Lei Shi / Luke W Guddat / Yan Gao / Zihe Rao / Zhiyong Lou / Abstract: Decoration of cap on viral RNA plays essential roles in SARS-CoV-2 proliferation. Here, we report a mechanism for SARS-CoV-2 RNA capping and document structural details at atomic resolution. The ...Decoration of cap on viral RNA plays essential roles in SARS-CoV-2 proliferation. Here, we report a mechanism for SARS-CoV-2 RNA capping and document structural details at atomic resolution. The NiRAN domain in polymerase catalyzes the covalent link of RNA 5' end to the first residue of nsp9 (termed as RNAylation), thus being an intermediate to form cap core (GpppA) with GTP catalyzed again by NiRAN. We also reveal that triphosphorylated nucleotide analog inhibitors can be bonded to nsp9 and fit into a previously unknown "Nuc-pocket" in NiRAN, thus inhibiting nsp9 RNAylation and formation of GpppA. S-loop (residues 50-KTN-52) in NiRAN presents a remarkable conformational shift observed in RTC bound with sofosbuvir monophosphate, reasoning an "induce-and-lock" mechanism to design inhibitors. These findings not only improve the understanding of SARS-CoV-2 RNA capping and the mode of action of NAIs but also provide a strategy to design antiviral drugs. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8gwb.cif.gz | 552.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8gwb.ent.gz | 440.5 KB | Display | PDB format |
PDBx/mmJSON format | 8gwb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8gwb_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 8gwb_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 8gwb_validation.xml.gz | 84.7 KB | Display | |
Data in CIF | 8gwb_validation.cif.gz | 127 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gw/8gwb ftp://data.pdbj.org/pub/pdb/validation_reports/gw/8gwb | HTTPS FTP |
-Related structure data
Related structure data | 34308MC 8gw1C 8gweC 8gwfC 8gwgC 8gwiC 8gwkC 8gwmC 8gwnC 8gwoC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Protein , 2 types, 3 molecules AFE
#1: Protein | Mass: 106780.977 Da / Num. of mol.: 1 / Fragment: UNP residues 4393-5324 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2 Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0DTD1, RNA-directed RNA polymerase |
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#4: Protein | Mass: 66930.531 Da / Num. of mol.: 2 / Fragment: UNP residues 5325-5925 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2 Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0DTD1 |
-Non-structural protein ... , 3 types, 4 molecules BDCG
#2: Protein | Mass: 21903.047 Da / Num. of mol.: 2 / Fragment: UNP residues 3943-4140 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2 Gene: rep, 1a-1b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0DTD1 #3: Protein | | Mass: 9248.804 Da / Num. of mol.: 1 / Fragment: UNP residues 3860-3942 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2 Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0DTC1 #5: Protein | | Mass: 12794.626 Da / Num. of mol.: 1 / Fragment: UNP residues 4141-4253 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2 Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0DTD1 |
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-RNA chain , 3 types, 3 molecules MIJ
#6: RNA chain | Mass: 590.414 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2 Production host: Escherichia coli BL21(DE3) (bacteria) |
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#7: RNA chain | Mass: 8172.932 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2 Production host: Escherichia coli BL21(DE3) (bacteria) |
#8: RNA chain | Mass: 10443.209 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2 Production host: Escherichia coli BL21(DE3) (bacteria) |
-Non-polymers , 3 types, 17 molecules
#9: Chemical | ChemComp-ZN / #10: Chemical | #11: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: E-RTC_RNA-nsp9 / Type: COMPLEX / Entity ID: #1-#3, #7-#8, #4-#6 / Source: RECOMBINANT |
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Source (natural) | Organism: Severe acute respiratory syndrome coronavirus 2 |
Source (recombinant) | Organism: Escherichia coli BL21(DE3) (bacteria) |
Buffer solution | pH: 7 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm |
Image recording | Electron dose: 60 e/Å2 / Film or detector model: GATAN K2 QUANTUM (4k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
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3D reconstruction | Resolution: 2.75 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1681356 / Symmetry type: POINT | ||||||||||||||||||||||||
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