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Yorodumi- PDB-8t12: Cryo-EM structure of DENV2 NS5 in complex with human STAT2 with t... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8t12 | ||||||
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Title | Cryo-EM structure of DENV2 NS5 in complex with human STAT2 with the N-terminal domain of STAT2 ordered. | ||||||
Components |
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Keywords | IMMUNE SYSTEM/VIRAL PROTEIN / complex / IMMUNE SYSTEM-VIRAL PROTEIN complex | ||||||
Function / homology | Function and homology information ISGF3 complex / negative regulation of type I interferon-mediated signaling pathway / regulation of mitochondrial fission / Interleukin-20 family signaling / type I interferon-mediated signaling pathway / ubiquitin-like protein ligase binding / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / cell surface receptor signaling pathway via JAK-STAT / host cell mitochondrion / Regulation of IFNA/IFNB signaling ...ISGF3 complex / negative regulation of type I interferon-mediated signaling pathway / regulation of mitochondrial fission / Interleukin-20 family signaling / type I interferon-mediated signaling pathway / ubiquitin-like protein ligase binding / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / cell surface receptor signaling pathway via JAK-STAT / host cell mitochondrion / Regulation of IFNA/IFNB signaling / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / ribonucleoside triphosphate phosphatase activity / regulation of protein phosphorylation / defense response / response to peptide hormone / RNA polymerase II transcription regulator complex / : / viral capsid / Interferon alpha/beta signaling / double-stranded RNA binding / protein complex oligomerization / monoatomic ion channel activity / regulation of cell population proliferation / clathrin-dependent endocytosis of virus by host cell / defense response to virus / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / Potential therapeutics for SARS / RNA helicase activity / host cell endoplasmic reticulum membrane / protein dimerization activity / DNA-binding transcription factor activity, RNA polymerase II-specific / induction by virus of host autophagy / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / viral RNA genome replication / RNA-dependent RNA polymerase activity / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / viral envelope / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / chromatin / virion attachment to host cell / regulation of transcription by RNA polymerase II / SARS-CoV-2 activates/modulates innate and adaptive immune responses / virion membrane / structural molecule activity / positive regulation of transcription by RNA polymerase II / proteolysis / extracellular region / nucleoplasm / ATP binding / membrane / identical protein binding / metal ion binding / nucleus / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Dengue virus type 2 | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.34 Å | ||||||
Authors | Biswal, M. / Lu, J. / Song, J. | ||||||
Funding support | United States, 1items
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Citation | Journal: To Be Published Title: Cryo-EM structure of DENV2 NS5 in complex with human STAT2 with the N-terminal domain of STAT2 ordered. Authors: Biswal, M. / Lu, J. / Song, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8t12.cif.gz | 284 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8t12.ent.gz | 222.2 KB | Display | PDB format |
PDBx/mmJSON format | 8t12.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t1/8t12 ftp://data.pdbj.org/pub/pdb/validation_reports/t1/8t12 | HTTPS FTP |
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-Related structure data
Related structure data | 40952MC 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
#1: Protein | Mass: 98025.031 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: STAT2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P52630 | ||
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#2: Protein | Mass: 103264.656 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Dengue virus type 2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q91H74 | ||
#3: Chemical | Has ligand of interest | Y | |
-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: complex of DENV2 NS5 and huamn STAT2 / Type: COMPLEX / Entity ID: #1-#2 / Source: MULTIPLE SOURCES | ||||||||||||
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Source (natural) |
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Source (recombinant) | Organism: Escherichia coli BL21(DE3) (bacteria) | ||||||||||||
Buffer solution | pH: 7.5 | ||||||||||||
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 FIELDBright-field microscopy / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 3.34 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 99938 / Symmetry type: POINT |