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Yorodumi- PDB-8frj: Structure of nsp14 N7-MethylTransferase domain fused with TELSAM ... -
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-Basic information
Entry | Database: PDB / ID: 8frj | ||||||
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Title | Structure of nsp14 N7-MethylTransferase domain fused with TELSAM bound to SGC0946 | ||||||
Components | Transcription factor ETV6,Guanine-N7 methyltransferase nsp14 chimera | ||||||
Keywords | VIRAL PROTEIN / N7-guanine methyl transferase / SARS-CoV-2 / nsp14 | ||||||
Function / homology | Function and homology information Signaling by membrane-tethered fusions of PDGFRA or PDGFRB / mesenchymal cell apoptotic process / vitellogenesis / hematopoietic stem cell proliferation / Signaling by FLT3 fusion proteins / neurogenesis / RNA polymerase II transcription regulatory region sequence-specific DNA binding / DNA-binding transcription repressor activity, RNA polymerase II-specific / protein guanylyltransferase activity / RNA endonuclease activity, producing 3'-phosphomonoesters ...Signaling by membrane-tethered fusions of PDGFRA or PDGFRB / mesenchymal cell apoptotic process / vitellogenesis / hematopoietic stem cell proliferation / Signaling by FLT3 fusion proteins / neurogenesis / RNA polymerase II transcription regulatory region sequence-specific DNA binding / DNA-binding transcription repressor activity, RNA polymerase II-specific / 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 / mRNA (guanine-N7)-methyltransferase / host cell Golgi apparatus / methyltransferase cap1 / DNA-binding transcription activator activity, RNA polymerase II-specific / symbiont-mediated perturbation of host ubiquitin-like protein modification / 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 perinuclear region of cytoplasm / host cell endoplasmic reticulum membrane / viral protein processing / lyase activity / DNA-binding transcription factor activity, RNA polymerase II-specific / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / RNA helicase / induction by virus of host autophagy / copper ion binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / RNA-directed RNA polymerase / DNA-binding transcription factor activity / protein domain specific binding / 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 / chromatin / nucleolus / regulation of transcription by RNA polymerase II / SARS-CoV-2 activates/modulates innate and adaptive immune responses / negative regulation of transcription by RNA polymerase II / ATP hydrolysis activity / proteolysis / RNA binding / zinc ion binding / ATP binding / membrane / nucleus / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Severe acute respiratory syndrome coronavirus 2 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.57 Å | ||||||
Authors | Kottur, J. / Aggarwal, A.K. | ||||||
Funding support | 1items
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Citation | Journal: Plos Pathog. / Year: 2023 Title: Structures of SARS-CoV-2 N7-methyltransferase with DOT1L and PRMT7 inhibitors provide a platform for new antivirals. Authors: Kottur, J. / White, K.M. / Rodriguez, M.L. / Rechkoblit, O. / Quintana-Feliciano, R. / Nayar, A. / Garcia-Sastre, A. / Aggarwal, A.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8frj.cif.gz | 217.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8frj.ent.gz | 142.7 KB | Display | PDB format |
PDBx/mmJSON format | 8frj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8frj_validation.pdf.gz | 670.6 KB | Display | wwPDB validaton report |
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Full document | 8frj_full_validation.pdf.gz | 671.9 KB | Display | |
Data in XML | 8frj_validation.xml.gz | 16.3 KB | Display | |
Data in CIF | 8frj_validation.cif.gz | 25.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fr/8frj ftp://data.pdbj.org/pub/pdb/validation_reports/fr/8frj | HTTPS FTP |
-Related structure data
Related structure data | 8frkC 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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Unit cell |
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-Components
#1: Protein | Mass: 35439.262 Da / Num. of mol.: 1 / Mutation: A4R, E67V, A77K Source method: isolated from a genetically manipulated source Details: Fusion protein containing TELSAM (uniprot P41212) and SARS-CoV-2 nsp14 N7-Methyl Transferase domain (P0DTD1) Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2 Gene: ETV6, TEL, TEL1, rep, 1a-1b / Production host: Escherichia coli (E. coli) References: UniProt: P41212, UniProt: P0DTD1, mRNA (guanine-N7)-methyltransferase, Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters |
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#2: Chemical | ChemComp-ZN / |
#3: Chemical | ChemComp-AW2 / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.36 Å3/Da / Density % sol: 47.89 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 11-17% Reagent Alcohol, 0.1-0.3M Lithium Sulfate and 0.1M Sodium Citrate pH 5.5 PH range: 5.1-6.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.979338 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 1, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979338 Å / Relative weight: 1 |
Reflection | Resolution: 1.57→54.595 Å / Num. obs: 31718 / % possible obs: 94.3 % / Redundancy: 10.2 % / Biso Wilson estimate: 20.91 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.105 / Rpim(I) all: 0.05 / Rrim(I) all: 0.116 / Net I/σ(I): 10.7 |
Reflection shell | Resolution: 1.57→1.711 Å / Rmerge(I) obs: 1.116 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 1588 / CC1/2: 0.618 / Rpim(I) all: 0.602 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.57→36.31 Å / SU ML: 0.1479 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 27.2803 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.79 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.57→36.31 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A
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