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Table of Contents for this page:

  • Current Issue
  • Advanced Online Publications Articles

  • Current Issue of Nature Structural and Molecular Biology

    Nature Structural aamp; Molecular Biology - Issue - nature.com science feeds

  • A 3D cellular context for the macromolecular world

  • We report the outcomes of the discussion initiated at the workshop entitled A 3D Cellular Context for the Macromolecular World and propose how data from emerging three-dimensional (3D) cellular imaging techniques—such as electron tomography, 3D scanning electron microscopy and soft X-ray tomography—should be archived, curated, validated and disseminated, to enable their interpretation and reuse by the biomedical community.

  • The timing is right

  • Yeast cells display synchronized oscillation between phases of high and low oxygen consumption accompanied by a program of cyclical gene expression. A study monitoring mRNA levels, histone modifications and chromatin occupancy of histone modifiers during the yeast metabolic cycle (YMC) at high temporal resolution reveals both 'just-in-time' supply of YMC gene products and new patterns of chromatin reconfiguration associated with transcriptional regulation.

  • Energetic dissection of Gleevec's selectivity toward human tyrosine kinases

  • Chemotherapeutic drug Gleevec (imatinib) is a potent and specific inhibitor of Abl kinase. NMR and fast kinetic analyses now reveal that Abl undergoes an induced-fit conformational change upon Gleevec binding.

  • High-temporal-resolution view of transcription and chromatin states across distinct metabolic states in budding yeast

  • Analyses of transcription and chromatin states during the yeast metabolic cycle reveal the links between different chromatin modifications and gene expression. The data also show that chromatin-modifier occupancies do not precisely match modification patterns.

  • Structure of cohesin subcomplex pinpoints direct shugoshin-Wapl antagonism in centromeric cohesion

  • The crystal structure of a human cohesin subcomplex, SA2–Scc1, guides mutagenesis analyses to dissect the antagonistic roles of shugoshin and Wapl in regulating centromeric functions during mitosis.

  • Mechanochemical basis of protein degradation by a double-ring AAA+ machine

  • A single-molecule optical-trapping approach is used to examine protein unfolding and translocation by double-ring AAA+ machine ClpA. Although ClpA can unfold some substrates faster than ClpX can, it translocates the unfolded polypeptide more slowly.

  • TRIM28 regulates RNA polymerase II promoter-proximal pausing and pause release

  • The protein TRIM28 is identified as a factor that modulates RNA polymerase II pausing and transcriptional elongation at a large number of mammalian genes. This function is regulated by transcription-coupled phosphorylation of TRIM28 at Ser824.

  • Visualization of recombination-mediated damage bypass by template switching

  • A combination of two-dimensional gel electrophoresis and EM is used to isolate and characterize multiple template-switching intermediates generated in budding yeast during replication of damaged DNA.

  • Protein dynamics during presynaptic-complex assembly on individual single-stranded DNA molecules

  • New single-molecule imaging analyses reveal how dynamic interactions of RPA, Rad52 and Rad51 on single-stranded DNA direct assembly of the presynaptic complex that promotes strand invasion during homologous recombination.

  • Rbfox3 controls the biogenesis of a subset of microRNAs

  • The RNA-binding protein Rbfox is an established regulator of alternative splicing. Here, Kawamoto and colleagues identify transcriptome-wide targets of Rbfox3 in neuronal cells and tissues to uncover an unexpected role in pri-miRNA processing

  • Cooperative structure of the heterotrimeric pre-mRNA retention and splicing complex

  • A solution NMR structure of the pre-mRNA retention and splicing (RES) core complex from budding yeast now reveals how the trimer stabilizes the RRM of its Snu17 subunit to promote pre-mRNA interactions within the spliceosome.

  • The RNA exosome promotes transcription termination of backtracked RNA polymerase II

  • New in vivo analyses in Schizosaccharomyces pombe suggest that the RNA exosome promotes transcription termination by targeting the 3' end of nascent transcripts associated with 'backtracked' RNA polymerase II, revealing a new link between mRNA surveillance and termination.

  • Uncovering global SUMOylation signaling networks in a site-specific manner

  • High-resolution MS identifies ggt;4,300 SUMOylation sites in ggt;1,600 proteins in human cells under standard growth conditions and after proteasome inhibition or heat shock. The data reveal cross-talk between SUMO and other post-translational modifications.

  • Multiple in vivo pathways for Escherichia coli small ribosomal subunit assembly occur on one pre-rRNA

  • Using the M2 stem-loop region to tag 16S pre-rRNA allows one-step isolation of assembly intermediates of the small ribosomal subunit from wild-type Escherichia coli. Characterization of these RNPs reveals multiple independent pathways for rRNA maturation.

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    Nature -Advance Online Publications

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    Nature Structural aamp; Molecular Biology - AOP - nature.com science feeds

  • Crystal structure of a SLC11 (NRAMP) transporter reveals the basis for transition-metal ion transport

  • The X-ray crystal structure of ScaDMT, a bacterial member of the solute carrier 11 transporter family, identifies conserved residues within the substrate-binding site that confer metal-ion selectivity.

  • Mechanisms for U2AF to define 3′ splice sites and regulate alternative splicing in the human genome

  • U2AF is known to affect 3A-splice-site selection. Here, Fu and colleagues use genome-wide analysis of U2AF-RNA interactions to define U2AF's key roles in gene expression and regulated splicing in normal and disease states.

  • MacroH2A1.1 and PARP-1 cooperate to regulate transcription by promoting CBP-mediated H2B acetylation

  • Histone variant macroH2A1 represses gene expression in heterochromatin. New data show that it can also stimulate transcription by cooperating with PARP-1 to promote CBP-mediated H2B acetylation and that this regulatory function is lost in cancer cells.

  • Cross-talking noncoding RNAs contribute to cell-specific neurodegeneration in SCA7

  • CAG-repeat expansion in the housekeeping gene ATXN7 causes the neurodegenerative disorder SCA7. Now ATXN7 protein is found to promote transcription and expression of miR-124, which in turn mediates cross-talk between lnc-SCA7 and ATXN7 transcripts.

  • A genome-wide map of adeno-associated virus–mediated human gene targeting

  • A genome-wide screen of gene targeting by an adeno-associated virus vector in human cells reveals that target sites are preferentially located where transcription occurs in the opposite direction from DNA replication, suggesting that colliding polymerases promote homologous recombination.

  • A mechanism for intracellular release of Na+ by neurotransmitter/sodium symporters

  • Crystal structures of MhsT, a bacterial member of the neurotransmitter/sodium symporter family, in an occluded, inward-facing state with bound sodium and substrate reveal conformational changes during the transport cycle that provide new insights into the mechanism of cytoplasmic sodium release.

  • Structure and mechanism of action of the BRCA2 breast cancer tumor suppressor

  • Structural and biochemical analyses of full-length human BRCA2 reveal how it facilitates RAD51-mediated homologous recombination to repair DNA double-strand breaks.

  • Crystal structures of free and antagonist-bound states of humanα9 nicotinic receptor extracellular domain

  • Crystal structures of the extracellular domain of human nAChR, in its apo form and with antagonists methyllycaconitine orα-bungarotoxin bound, are presented. The structures provide insight into the channel-opening mechanism of nAChRs and their pharmacological properties.

  • Crystal structure of the vitamin B3 transporter PnuC, a full-length SWEET homolog

  • An X-ray crystal structure of substrate-bound Neisseria PnuC, a bacterial member of the SWEET family of transporters, provides key insights into the translocation mechanism and potential evolution of these membrane proteins.
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