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The formation of stable 18S U11/U12 di-snRNPs before their association with the pre-mRNA is a characteristic feature of the minor spliceosome. During the spliceosomal assembly, the 18S snRNP binds cooperatively to the introns' 5′ splice and branch point site. The molecular basis for this recognition is still unknown. Here, we report the solution structure of the U11-48K CHHC Zn finger, a domain unique...
The minichromosome maintenance (MCM) proteins, members of the AAA+ (ATPase associated with diverse cellular activities) superfamily, are believed to constitute the replicative helicase in eukaryotic and archaeal species. Here, we present the 1.9 Å resolution crystal structure of a monomeric MCM homolog from Methanopyrus kandleri, the first crystallographic structure of a full-length MCM. We also present...
Comprehensive knowledge of protein-ligand interactions should provide a useful basis for annotating protein functions, studying protein evolution, engineering enzymatic activity, and designing drugs. To investigate the diversity and universality of ligand-binding sites in protein structures, we conducted the all-against-all atomic-level structural comparison of over 180,000 ligand-binding sites found...
The pH-controlled M2 protein from influenza A is a critical component of the virus and serves as a target for the aminoadamantane antiflu agents that block its H + channel activity. To better understand its H + gating mechanism, we investigated M2 in lipid bilayers with a new combination of IR spectroscopies and theory. Linear Fourier transform infrared (FTIR) spectroscopy was used...
We describe the proceedings and conclusions from the “Workshop on Applications of Protein Models in Biomedical Research” (the Workshop) that was held at the University of California, San Francisco on 11 and 12 July, 2008. At the Workshop, international scientists involved with structure modeling explored (i) how models are currently used in biomedical research, (ii) the requirements and challenges...
The crystal structures of two homologous endopeptidases from cyanobacteria Anabaena variabilis and Nostoc punctiforme were determined at 1.05 and 1.60 Å resolution, respectively, and contain a bacterial SH3-like domain (SH3b) and a ubiquitous cell-wall-associated NlpC/P60 (or CHAP) cysteine peptidase domain. The NlpC/P60 domain is a primitive, papain-like peptidase in the CA clan of cysteine peptidases...
Secretins are among the largest bacterial outer membrane proteins known. Here we report the crystal structure of the periplasmic N-terminal domain of GspD (peri-GspD) from the type 2 secretion system (T2SS) secretin in complex with a nanobody, the VHH domain of a heavy-chain camelid antibody. Two different crystal forms contained the same compact peri-GspD:nanobody heterotetramer. The nanobody contacts...
Interaction of viral protein gp42 with its receptor is the trigger for the entry of Epstein-Barr virus into B cells. The structure of gp42 reported by Kirschner et al. (2009) in this issue of Structure suggests a likely triggering mechanism substantially different from that of a related herpesvirus.
In response to the intercellular messenger ATP, P2X receptors transfer various sensory information, including pain. Here we have reconstructed the structure of the P2X 2 receptor at 15 Å resolution from more than 90,000 particle images, taken with a cryo-electron microscope equipped with a helium-cooled stage. This three-dimensional depiction, presumably in a closed state, revealed an elongated...
Poly(A)-specific ribonuclease (PARN) is a homodimeric, processive, and cap-interacting 3′ exoribonuclease that efficiently degrades eukaryotic mRNA poly(A) tails. The crystal structure of a C-terminally truncated PARN in complex with m 7 GpppG reveals that, in one subunit, m 7 GpppG binds to a cavity formed by the RRM domain and the nuclease domain, whereas in the other subunit, it...
Ever since the discovery of the nucleosome in 1974, scientists have stumbled upon discrete particles in which DNA is wrapped around histone complexes of different stoichiometries: octasomes, hexasomes, tetrasomes, “split” half-nucleosomes, and, recently, bona fide hemisomes. Do all these particles exist in vivo? Under what conditions? What is their physiological significance in the complex DNA transactions...
Coactivators CREB-binding protein and p300 play important roles in mediating the transcriptional activity of p53. Until now, however, no detailed structural information has been available on how any of the domains of p300 interact with p53. Here, we report the NMR structure of the complex of the Taz2 (C/H3) domain of p300 and the N-terminal transactivation domain of p53. In the complex, p53 forms...
The automated building of a protein model into an electron density map remains a challenging problem. In the ARP/wARP approach, model building is facilitated by initially interpreting a density map with free atoms of unknown chemical identity; all structural information for such chemically unassigned atoms is discarded. Here, this is remedied by applying restraints between free atoms, and between...
1D and 2D-IR spectroscopy was used to resolve the structural transition that is responsible for the gating mechanism of the influenza A M2 channel (Manor et al., 2009). This report constitutes a milestone in the development of both ATR-FTIR and 2D-IR spectroscopies as precise tools for structural biology.
The chaperonin GroEL interacts with various proteins, leading them to adopt their correct conformations with the aid of GroES and ATP. The actual mechanism is still being debated. In this study, by use of cryo-electron microscopy, we determined the solution structure of the Thermus thermophilus GroEL-GroES complex encapsulating its substrate proteins. We observed the averaged density of substrate...
The signal transduction ATPases with numerous domains (STAND) represent a newly recognized class of widespread, sophisticated ATPases that are related to the AAA+ proteins and that function as signaling hubs. These proteins control diverse biological processes in bacteria and eukaryotes, including gene expression, apoptosis, and innate immunity responses. They function as tightly regulated switches,...
Histidine kinase receptors are a large family of membrane-spanning proteins found in many prokaryotes and some eukaryotes. They are a part of two-component signal transduction systems, which each comprise a sensor kinase and a response regulator and are involved with the regulation of many cellular processes. NarX is a histidine kinase receptor that responds to nitrate and nitrite to effect regulation...
Epstein-Barr virus requires glycoproteins gH/gL, gB, and gp42 to fuse its lipid envelope with B cells. Gp42 is a type II membrane protein consisting of a flexible N-terminal region, which binds gH/gL, and a C-terminal lectin-like domain that binds to the B-cell entry receptor human leukocyte antigen (HLA) class II. Gp42 triggers membrane fusion after HLA binding, a process that requires simultaneous...
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