9eab | pdb_00009eab

Seneca valley virus Altered particle at physiological condition (A-particle[P])

spinqualitylabelsall models 9eab, resolution 3.39Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 9eab is a 4 chain structure with sequence from Seneca Valley virus USA/SSV-001. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Method: Electron Microscopy, Resolution 3.39Å Ligands: CA Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Function POLG_SVV1 Forms an icosahedral capsid of pseudo T=3 symmetry with capsid proteins VP2 and VP3 (PubMed:18940610). Together they form an icosahedral capsid composed of 60 copies of each VP1, VP2, and VP3, with a diameter of approximately 325 Angstroms (Probable). VP4 lies on the inner surface of the protein shell formed by VP1, VP2 and VP3 (By similarity). All the three latter proteins contain a beta-sheet structure called beta-barrel jelly roll (By similarity). VP1 is situated at the 12 fivefold axes, whereas VP2 and VP3 are located at the quasi-sixfold axes (PubMed:18940610). Binds the host receptor ANTXR1 for attachment and uncoating (entry) (PubMed:30381454, PubMed:30514821).[UniProtKB:P12296] Forms an icosahedral capsid of pseudo T=3 symmetry with capsid proteins VP2 and VP3 (PubMed:18940610). Together they form an icosahedral capsid composed of 60 copies of each VP1, VP2, and VP3, with a diameter of approximately 270 Angstroms (Probable). VP4 lies on the inner surface of the protein shell formed by VP1, VP2 and VP3 (By similarity). All the three latter proteins contain a beta-sheet structure called beta-barrel jelly roll (By similarity). VP1 is situated at the 12 fivefold axes, whereas VP2 and VP3 are located at the quasi-sixfold axes (PubMed:18940610). Binds the host receptor ANTXR1 for attachment and uncoating (entry) (PubMed:30381454, PubMed:30514821).[UniProtKB:P12296] Forms an icosahedral capsid of pseudo T=3 symmetry with capsid proteins VP2 and VP3 (Probable). Together they form an icosahedral capsid composed of 60 copies of each VP1, VP2, and VP3, with a diameter of approximately 270 Angstroms (Probable). VP4 lies on the inner surface of the protein shell formed by VP1, VP2 and VP3. All the three latter proteins contain a beta-sheet structure called beta-barrel jelly roll (By similarity). VP1 is situated at the 12 fivefold axes, whereas VP2 and VP3 are located at the quasi-sixfold axes (By similarity). Vp3 also seems to be involved in the binding to host receptor ANTXR1 for attachment and uncoating (entry) (PubMed:30381454).[UniProtKB:P12296] Lies on the inner surface of the capsid shell (PubMed:18940610). After binding to the host receptor, the capsid undergoes conformational changes (By similarity). Capsid protein VP4 is released, capsid protein VP1 N-terminus is externalized, and together, they shape a pore in the host membrane through which the viral genome is translocated into the host cell cytoplasm (By similarity). After genome has been released, the channel shrinks (By similarity).[UniProtKB:P12296] VP0 precursor is a component of immature procapsids.[UniProtKB:P08617] Mediates self-processing of the polyprotein by a translational effect termed 'ribosome skipping'. Mechanistically, 2A-mediated cleavage occurs between the C-terminal glycine and the proline of the downstream protein 2B.[UniProtKB:P03305] Plays an essential role in the virus replication cycle by acting as a viroporin. Creates a pore in the host endoplasmic reticulum and as a consequence releases Ca2+ in the cytoplasm of infected cell. In turn, high levels of cytoplasmic calcium may trigger membrane trafficking and transport of viral ER-associated proteins to viroplasms, sites of viral genome replication.[UniProtKB:P03305] Associates with and induces structural rearrangements of intracellular membranes.[UniProtKB:P03305] Covalently linked to the 5'-end of both the positive-strand and negative-strand genomic RNAs. Acts as a genome-linked replication primer.[UniProtKB:P03305] Cysteine protease that generates mature viral proteins from the precursor polyprotein (By similarity). Inactivates crucial host adapter molecules in order to suppress antiviral type-I interferon (type-I IFN) and NF-kappaB production to escape host antiviral innate immune responses (PubMed:28566380, PubMed:29427864, PubMed:30408499). Deubiquitinase that acts on both lysine-48- and lysine-63-linked polyubiquitin chains and inhibits the ubiquitination of the ATP-dependent RNA helicase RIGI, TANK-binding kinase 1 (TBK1), and TNF receptor-associated factor 3 (TRAF3), thereby blocking the expression of IFN-beta and IFN stimulated gene 54 (ISG54) (PubMed:30408499). Induces host IRF3 and IRF7 degradation thereby suppressing IRF3- and IRF7-induced type-I IFN production (PubMed:29427864). Also decreases host IRF3 phosphorylation leading to negligible IRF3 activation (PubMed:29427864). Cleaves host MAVS, TRIF and TANK, which are then unable to regulate pattern recognition receptor (PRR)-mediated type-I IFN production (PubMed:28566380). Inhibits the integrated stress response (ISR) in the infected cell by disrupting eIF4GI-G3BP1 interaction (PubMed:33133097). Stress granule formation is thus inhibited (PubMed:33133097).[UniProtKB:P12296] Replicates the genomic and antigenomic RNAs by recognizing replications specific signals (By similarity). Performs VPg uridylylation (By similarity).[UniProtKB:P12296]

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