Cryoelectron microscopy has been used to determine the structure of a virus when complexed with its glycoprotein cellular receptor. Human rhinovirus 16 complexed with the two amino-terminal, immunoglobulln-like domains of the intercellular adhesion molecule 1 shows that the intercellular adhesion molecule 1 binds into the 12-A deep "canyon" on the viral surface. This result confirms the prediction that the viral-receptor attachment site lies in a cavity inaccessible to the host's antibodies. The atomic structures of human rhinovirus 14 and CD4, homologous to human rhinovirus 16 and intercellular adhesion molecule 1, showed excellent correspondence with observed density, thus establishing the virus-receptor interactions.Human rhinoviruses are one of the major causes of the common cold. They, like other picornaviruses, are icosahedral assemblies of 60 protomers that envelope a single, positivesense strand of RNA. Each protomer consists of four polypeptides, VP1-VP4. The three external viral proteins (VP1-VP3) each have an approximate Mr of 30,000 and a similar folding topology (1, 2). The external viral radius is "'150 A, and the total molecular weight is roughly 8.5 x 106. A surface depression, or canyon, that is "12 A deep and 12-15 A wide, encircles each pentagonal vertex (Fig. lc). Residues lining the canyon are more conserved than other surface residues among rhinovirus serotypes (5). The most variable surface residues are at the sites of attachment of neutralizing antibodies (1, 6, 7). It has been proposed that the cellular receptor molecule recognized by the virus binds to conserved residues in the canyon, thus escaping neutralization by host antibodies that are too big to penetrate into that region. This hypothesis (1, 8) is supported by site-directed mutagenesis ofresidues lining the canyon that alters the ability ofthe virus to attach to HeLa cell membranes (9). Also, conformational changes in the canyon floor, produced by certain antiviral agents that bind into a pocket beneath the canyon floor, inhibit viral attachment to cellular membranes (10). Conservation ofthe viral-attachment site inside a surface depression has been observed for Mengo (11) and influenza virus (12).There are well over 100 human rhinovirus serotypes, which can be divided into roughly two groups according to the cellular receptor they recognize (13,14). The structures of human rhinovirus 14 (HRV-14) (1), which belongs to the major group of serotypes, and of HRV-1A (15), which belongs to the minor group of serotypes, have been determined. There are at least 78 serotypes (16) that bind to intercellular adhesion molecule 1 (ICAM-1), the major group rhinovirus receptor (17, 18). The ICAM-1 molecule has five immunoglobulin-like domains (D1-D5, numbered sequentially from the amino end), a transmembrane portion, and a small cytoplasmic domain (19, 20). Domains D2, D3, and D4 are glycosylated. Unlike immunoglobulins, ICAM-1 appears to be monomeric (18). Mutational analysis of ICAM-1 has shown that domain D1 contains the primary b...

X-ray diffraction data were collected from human rhinovirus 14 crystals a few minutes after exposure to acid vapor and prior to excessive crystalline disorder. Conformational changes occurred (i) in the GH loop of viral protein (VP) 1, (it) at the ion binding site on the outer surface of the pentamer center, and (us) in VP3 and VP4 on the virion's interior in the vicinity of the fivefold axis. Amino acid substitutions in mutants resistant to low pH, or to drugs that inhibit uncoating, were concentrated in the vicinity of the GH loop. It is proposed that the acid-induced changes reflect processes that trigger uncoating.

The transcription factor (TF) SOX18 drives lymphatic vessel development in both embryogenesis and tumour-induced neo-lymphangiogenesis. Genetic disruption of Sox18 in a mouse model protects from tumour metastasis and established the SOX18 protein as a molecular target. Here, we report the crystal structure of the SOX18 DNA binding high-mobility group (HMG) box bound to a DNA element regulating Prox1 transcription. The crystals diffracted to 1.75Å presenting the highest resolution structure of a SOX/DNA complex presently available revealing water structure, structural adjustments at the DNA contact interface and non-canonical conformations of the DNA backbone. To explore alternatives to challenging small molecule approaches for targeting the DNA-binding activity of SOX18, we designed a set of five decoys based on modified Prox1-DNA. Four decoys potently inhibited DNA binding of SOX18 in vitro and did not interact with non-SOX TFs. Serum stability, nuclease resistance and thermal denaturation assays demonstrated that a decoy circularized with a hexaethylene glycol linker and terminal phosphorothioate modifications is most stable. This SOX decoy also interfered with the expression of a luciferase reporter under control of a SOX18-dependent VCAM1 promoter in COS7 cells. Collectively, we propose SOX decoys as potential strategy for inhibiting SOX18 activity to disrupt tumour-induced neo-lymphangiogenesis.

BackgroundPHF21A has been associated with intellectual disability and craniofacial anomalies based on its deletion in the Potocki-Shaffer syndrome region at 11p11.2 and its disruption in three patients with balanced translocations. In addition, three patients with de novo truncating mutations in PHF21A were reported recently. Here, we analyze genomic data from seven unrelated individuals with mutations in PHF21A and provide detailed clinical descriptions, further expanding the phenotype associated with PHF21A haploinsufficiency.MethodsDiagnostic trio whole exome sequencing, Sanger sequencing, use of GeneMatcher, targeted gene panel sequencing, and MiSeq sequencing techniques were used to identify and confirm variants. RT-qPCR was used to measure the normal expression pattern of PHF21A in multiple human tissues including 13 different brain tissues. Protein-DNA modeling was performed to substantiate the pathogenicity of the missense mutation.ResultsWe have identified seven heterozygous coding mutations, among which six are de novo (not maternal in one). Mutations include four frameshifts, one nonsense mutation in two patients, and one heterozygous missense mutation in the AT Hook domain, predicted to be deleterious and likely to cause loss of PHF21A function. We also found a new C-terminal domain composed of an intrinsically disordered region. This domain is truncated in six patients and thus likely to play an important role in the function of PHF21A, suggesting that haploinsufficiency is the likely underlying mechanism in the phenotype of seven patients. Our results extend the phenotypic spectrum of PHF21A mutations by adding autism spectrum disorder, epilepsy, hypotonia, and neurobehavioral problems. Furthermore, PHF21A is highly expressed in the human fetal brain, which is consistent with the neurodevelopmental phenotype.ConclusionDeleterious nonsense, frameshift, and missense mutations disrupting the AT Hook domain and/or an intrinsically disordered region in PHF21A were found to be associated with autism spectrum disorder, epilepsy, hypotonia, neurobehavioral problems, tapering fingers, clinodactyly, and syndactyly, in addition to intellectual disability and craniofacial anomalies. This suggests that PHF21A is involved in autism spectrum disorder and intellectual disability, and its haploinsufficiency causes a diverse neurological phenotype.Electronic supplementary materialThe online version of this article (10.1186/s13229-019-0286-0) contains supplementary material, which is available to authorized users.