3jb4

Structure of Ljungan virus: insight into picornavirus packagingStructure of Ljungan virus: insight into picornavirus packaging

3jb4, resolution 3.80Å Show:Asymmetric Unit Biological Assembly Structural highlights 3jb4 is a 3 chain structure with sequence from Ljungan virus 87-012. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Method: Electron Microscopy, Resolution 3.8Å Experimental data: Check Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Function POLG_LJUV1 Forms an icosahedral capsid of pseudo T=3 symmetry together with capsid proteins VP1 and VP3 (PubMed:26446437). The capsid is 300 Angstroms in diameter, composed of 60 copies of each capsid protein and enclosing the viral positive strand RNA genome (PubMed:26446437). The attachment to the host cell receptor induces virion internalization predominantly through clathrin-mediated endocytosis (By similarity). Binds packaging signals present in the viral RNA (By similarity).[UniProtKB:Q66578] Forms an icosahedral capsid of pseudo T=3 symmetry together with capsid proteins VP0 and VP1 (PubMed:26446437). The capsid is 300 Angstroms in diameter, composed of 60 copies of each capsid protein and enclosing the viral positive strand RNA genome (PubMed:26446437). The attachment to the host cell receptor induces virion internalization predominantly through clathrin-mediated endocytosis (By similarity). Binds packaging signals present in the viral RNA (By similarity).[UniProtKB:Q66578] Forms an icosahedral capsid of pseudo T=3 symmetry together with capsid proteins VP0 and VP3 (PubMed:26446437). The capsid is 300 Angstroms in diameter, composed of 60 copies of each capsid protein and enclosing the viral positive strand RNA genome (PubMed:26446437). The attachment to the host cell receptor induces virion internalization predominantly through clathrin-mediated endocytosis (By similarity). Binds packaging signals present in the viral RNA (By similarity).[UniProtKB:Q66578] Mediates self-processing of the polyprotein by a translational effect termed 'ribosome skipping'. Mechanistically, 2A1-mediated cleavage occurs between the C-terminal glycine and the proline of the downstream protein 2A2. Plays an essential role in the virus replication cycle by acting as a viroporin. Creates a pore in the host reticulum endoplasmic 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:P03300] Induces and associates with structural rearrangements of intracellular membranes. Displays RNA-binding, nucleotide binding and NTPase activities. May play a role in virion morphogenesis and viral RNA encapsidation by interacting with the capsid protein VP3.[UniProtKB:P03300] Localizes the viral replication complex to the surface of membranous vesicles (By similarity). It inhibits host cell endoplasmic reticulum-to-Golgi apparatus transport and causes the disassembly of the Golgi complex, possibly through GBF1 interaction (By similarity). This would result in depletion of MHC, trail receptors and IFN receptors at the host cell surface (By similarity). Plays an essential role in viral RNA replication by recruiting ACBD3 and PI4KB at the viral replication sites, thereby allowing the formation of the rearranged membranous structures where viral replication takes place (By similarity).[UniProtKB:P03300][UniProtKB:Q9YLG5] Acts as a primer for viral RNA replication and remains covalently bound to viral genomic RNA. VPg is uridylylated prior to priming replication into VPg-pUpU. The VPg-pUpU is then used as primer on the genomic RNA poly(A) by the RNA-dependent RNA polymerase to replicate the viral genome. Following genome release from the infecting virion in the cytoplasm, the VPg-RNA linkage is probably removed by host TDP2. During the late stage of the replication cycle, host TDP2 is excluded from sites of viral RNA synthesis and encapsidation, allowing for the generation of progeny virions.[UniProtKB:P03300] Cysteine protease that generates mature viral proteins from the precursor polyprotein (By similarity). In addition to its proteolytic activity, it binds to viral RNA, and thus influences viral genome replication. RNA and substrate bind cooperatively to the protease (By similarity).[UniProtKB:P03304][UniProtKB:P12296] Replicates the viral genomic RNA on the surface of intracellular membranes. Covalently attaches UMP to a tyrosine of VPg, which is used to prime RNA synthesis. The positive stranded RNA genome is first replicated at virus induced membranous vesicles, creating a dsRNA genomic replication form. This dsRNA is then used as template to synthesize positive stranded RNA genomes. ss(+)RNA genomes are either translated, replicated or encapsidated.[UniProtKB:P03300] Publication Abstract from PubMed Picornaviruses are responsible for a range of human and animal diseases, but how their RNA genome is packaged remains poorly understood. A particularly poorly studied group within this family are those that lack the internal coat protein, VP4. Here we report the atomic structure of one such virus, Ljungan virus, the type member of the genus Parechovirus B, which has been linked to diabetes and myocarditis in humans. The 3.78-A resolution cryo-electron microscopy structure shows remarkable features, including an extended VP1 C terminus, forming a major protuberance on the outer surface of the virus, and a basic motif at the N terminus of VP3, binding to which orders some 12% of the viral genome. This apparently charge-driven RNA attachment suggests that this branch of the picornaviruses uses a different mechanism of genome encapsidation, perhaps explored early in the evolution of picornaviruses. Structure of Ljungan virus provides insight into genome packaging of this picornavirus.,Zhu L, Wang X, Ren J, Porta C, Wenham H, Ekstrom JO, Panjwani A, Knowles NJ, Kotecha A, Siebert CA, Lindberg AM, Fry EE, Rao Z, Tuthill TJ, Stuart DI Nat Commun. 2015 Oct 8;6:8316. doi: 10.1038/ncomms9316. PMID:26446437 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.