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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

  • Mechanisms for targeted, purposeful mutation revealed in an APOBEC–DNA complex

  • Targeted deamination of cytosine bases in DNA by AID/APOBEC-family enzymes is critical for proper immune function, but it also poses risks to genomic integrity. New structures reported by Harris, Aihara and colleagues offer the first glimpses into the enzyme–DNA complex and reveal both expected and unexpected insights into the DNA-binding mode involved in targeting purposeful mutation.

  • Histone degradation in response to DNA damage enhances chromatin dynamics and recombination rates

  • A combination of SILAC-MS, genome-wide nucleosome mapping and live-cell imaging reveal rapid histone degradation and global chromatin decompaction after the induction of DNA double-strand breaks in S. cerevisiae.

  • Crystal structures of human glycine receptorα3 bound to a novel class of analgesic potentiators

  • The structure of GlyRα3 in complex with a selective potentiator that decreases neuropathic pain in an animal model identifies a novel allosteric regulatory mechanism.

  • Structure of the polycystic kidney disease TRP channel Polycystin-2 (PC2)

  • The cryo-EM structure of human polycystin-2 (PC2) in a closed conformation reveals a domain located above the pore filter, forming an upper vestibule and making contacts with the pore and voltage-sensor-like domains.

  • Molecular insights into lipid-assisted Ca2+ regulation of the TRP channel Polycystin-2

  • Cryo-EM structures of full-length human PC2 reveal two distinct channel states: an open conformation and a blocked conformation with Ca2+ bound at the entrance of the selectivity filter.

  • Structural basis for targeted DNA cytosine deamination and mutagenesis by APOBEC3A and APOBEC3B

  • Crystal structures of human APOBEC3A and a chimera of APOBEC3B and APOBEC3A bound to ssDNA reveal an unanticipated‘U-shaped’ binding mode and provide insight into target selectivity.

  • Self-correcting mismatches during high-fidelity DNA replication

  • Cryo-EM and NMR analyses of the E. coli replisome show how DNA-end fraying after mismatch incorporation at the polymerase active site enables substrate ends to reach the‘proofreading’ exonuclease site for mismatch removal.

  • Structural insights into a unique Hsp70-Hsp40 interaction in the eukaryotic ribosome-associated complex

  • The yeast ribosome-associated complex (RAC) is formed by Hsp40 protein Zuo1 and the atypical Hsp70 chaperone Ssz1. Structural analyses show Ssz1 in a hybrid conformation between the open and closed state and its substrate-binding domain completed by Zuo1.

  • Molecular architecture and dynamics of ASH1 mRNA recognition by its mRNA-transport complex

  • Crystal structures of a localization element of ASH1 mRNA alone, in complex with its nuclear shuttling protein She2p, and in the cytoplasmic complex with She2p and She3p reveal a step-wise maturation pathway.

  • Pif1-family helicases cooperatively suppress widespread replication-fork arrest at tRNA genes

  • Genome-wide analyses of S. cerevisiae replisome mobility reveal overlapping roles of Pif1 and Rrm3 helicases in alleviating replication-fork arrest at tRNA genes.

  • Crystal structure of the MOP flippase MurJ in an inward-facing conformation

  • The crystal structure of MurJ, a bacterial lipid II flippase involved in peptidoglycan biosynthesis and a member of the MOP transporter superfamily, reveals an inward-facing conformation and points to an alternating-access mechanism.

  • Structural insights into the secretin translocation channel in the type II secretion system

  • Cryo-EM structures of secretin GspD in type II secretion systems from Escherichia coli and Vibrio cholera reveal a pentadecameric architecture, with three rings in the periplasm andβ-strand-enriched gates on the outer membrane.

  • Structure of the immature Zika virus at 9Å resolution

  • The cryo-EM structure of immature Zika virus shows partially ordered capsid proteins and reveals differences between pre-epidemic and epidemic strains at protein interfaces within the trimeric spikes.

  • Solution structure of discoidal high-density lipoprotein particles with a shortened apolipoprotein A-I

  • HDL particles transport cholesterol and contain apolipoprotein A-I as their major protein. The solution structure of discoidal HDL particles reconstituted with a shortened apoA-I is now solved via a combination of NMR and EPR analyses.

  • Corrigendum: Exon-intron circular RNAs regulate transcription in the nucleus

  • Erratum: Selective integrin endocytosis is driven by interactions between the integrinα-chain and AP2

  • Erratum: BRD4 is a histone acetyltransferase that evicts nucleosomes from chromatin

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    Nature -Advance Online Publications

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

  • Mechanism and timing of Mcm2–7 ring closure during DNA replication origin licensing

  • smFRET analysis and colocalization spectroscopy reveal the mechanism of DNA entry into the Mcm2–7 helicase ring during replication origin licensing.

  • Structural basis of Mcm2–7 replicative helicase loading by ORC–Cdc6 and Cdt1

  • A 3.9-Å-resolution cryo-EM structure of the S. cerevisiae OCCM replicative helicase loading complex bound to DNA shows how ORC and Cdc6 recognize DNA origins, and reveals details of how the Mcm2–7 hexamer ring is loaded onto the DNA helix.

  • Open-ringed structure of the Cdt1–Mcm2–7 complex as a precursor of the MCM double hexamer

  • A high-resolution cryo-EM structure of the heptameric Cdt1–Mcm2–7 complex of the replicative helicase from budding yeast suggests a ‘spring-action’ DNA-unwinding mechanism.

  • STAT2 is an essential adaptor in USP18-mediated suppression of type I interferon signaling

  • STAT2, previously known as a positive effector of interferon signaling, is now shown to participate in negative feedback and suppression of this signaling pathway, by recruiting USP18 to the type I IFN receptor subunit IFNAR2.

  • Structural basis of the specificity of USP18 toward ISG15

  • The specificity of USP18's deconjugating activity toward ISG15, a ubiquitin-like protein induced by interferon, is revealed by structural and biochemistry studies of the mouse proteins.

  • RdRP-synthesized antisense ribosomal siRNAs silence pre-rRNA via the nuclear RNAi pathway

  • A genetic screen in C. elegans identifies a suppressor of siRNA and a new subset of 22G-RNAs that act through the nuclear RNAi pathway to downregulate pre-rRNA under stress conditions.

  • Xist-dependent imprinted X inactivation and the early developmental consequences of its failure

  • Single-cell RNA sequencing of preimplantation mouse embryos demonstrates that lack of paternal Xist leads to genome-wide transcriptional misregulation in the early blastocyst and a failure to activate the extraembryonic pathway.

  • The evolutionary capacitor HSP90 buffers the regulatory effects of mammalian endogenous retroviruses

  • The molecular chaperone HSP90 is found to affect the expression of mouse endogenous retrovirus elements and neighboring genes through the KAP1–SETDB1 epigenetic-repression machinery.

  • Eukaryotic Rad50 functions as a rod-shaped dimer

  • Structural, biochemical and in vivo analyses reveal that Rad50 zinc-hook and coiled-coil domains form a novel dimerization interface essential for Mre11-complex function in DNA damage response and repair.

  • G-quadruplex structures within the 3′ UTR of LINE-1 elements stimulate retrotransposition

  • Guanine-rich sequences with a tendency to form G4 structures are a hallmark of hominoid-specific L1 retrotransposons, and their stabilization increases L1 mobility, thus potentially affecting genome evolution.

  • Structural basis of dual Ca2+/pH regulation of the endolysosomal TRPML1 channel

  • Crystal structures of the linker region of TRPML1 reveal that the luminal domain forms a tetrameric pore. Along with electrophysiology studies, this work provides insight into the mechanism of channel regulation by Ca2+ and H+.

  • Structural snapshot of cytoplasmic pre-60S ribosomal particles bound by Nmd3, Lsg1, Tif6 and Reh1

  • The cryo-EM structure of pre-60S purified via Nmd3 provides molecular insights into the roles of assembly factors Nmd3, Lsg1, Tif6 and Reh1 in the last steps of ribosomal large-subunit maturation.

  • Cotranslational folding of spectrin domains via partially structured states

  • Using a family of spectrin domain variants and a combination of structural, biochemical and biophysical approaches, it is shown that cotranslational folding cannot be predicted on the basis of the folding behavior of isolated proteins.

  • The gastrula transition reorganizes replication-origin selection in Caenorhabditis elegans

  • Nascent-strand mapping of active DNA replication origins before and after gastrulation in C. elegans reveals that replication initiation is coordinated with transcriptional programs during embryonic development.

  • Molecular architecture and dynamics of ASH1 mRNA recognition by its mRNA-transport complex

  • Crystal structures of a localization element of ASH1 mRNA alone, in complex with its nuclear shuttling protein She2p, and in the cytoplasmic complex with She2p and She3p reveal a step-wise maturation pathway.

  • Molecular insights into lipid-assisted Ca2+ regulation of the TRP channel Polycystin-2

  • Cryo-EM structures of full-length human PC2 reveal two distinct channel states: an open conformation and a blocked conformation with Ca2+ bound at the entrance of the selectivity filter.

  • Self-correcting mismatches during high-fidelity DNA replication

  • Cryo-EM and NMR analyses of the E. coli replisome show how DNA-end fraying after mismatch incorporation at the polymerase active site enables substrate ends to reach the‘proofreading’ exonuclease site for mismatch removal.

  • Histone degradation in response to DNA damage enhances chromatin dynamics and recombination rates

  • A combination of SILAC-MS, genome-wide nucleosome mapping and live-cell imaging reveal rapid histone degradation and global chromatin decompaction after the induction of DNA double-strand breaks in S. cerevisiae.

  • Structure of the immature Zika virus at 9Å resolution

  • The cryo-EM structure of immature Zika virus shows partially ordered capsid proteins and reveals differences between pre-epidemic and epidemic strains at protein interfaces within the trimeric spikes.

  • Structural insights into a unique Hsp70-Hsp40 interaction in the eukaryotic ribosome-associated complex

  • The yeast ribosome-associated complex (RAC) is formed by Hsp40 protein Zuo1 and the atypical Hsp70 chaperone Ssz1. Structural analyses show Ssz1 in a hybrid conformation between the open and closed state and its substrate-binding domain completed by Zuo1.

  • Structural insights into the secretin translocation channel in the type II secretion system

  • Cryo-EM structures of secretin GspD in type II secretion systems from Escherichia coli and Vibrio cholera reveal a pentadecameric architecture, with three rings in the periplasm andβ-strand-enriched gates on the outer membrane.

  • Solution structure of discoidal high-density lipoprotein particles with a shortened apolipoprotein A-I

  • HDL particles transport cholesterol and contain apolipoprotein A-I as their major protein. The solution structure of discoidal HDL particles reconstituted with a shortened apoA-I is now solved via a combination of NMR and EPR analyses.

  • Crystal structure of the MOP flippase MurJ in an inward-facing conformation

  • The crystal structure of MurJ, a bacterial lipid II flippase involved in peptidoglycan biosynthesis and a member of the MOP transporter superfamily, reveals an inward-facing conformation and points to an alternating-access mechanism.

  • Structure of the polycystic kidney disease TRP channel Polycystin-2 (PC2)

  • The cryo-EM structure of human polycystin-2 (PC2) in a closed conformation reveals a domain located above the pore filter, forming an upper vestibule and making contacts with the pore and voltage-sensor-like domains.

  • Crystal structures of human glycine receptorα3 bound to a novel class of analgesic potentiators

  • The structure of GlyRα3 in complex with a selective potentiator that decreases neuropathic pain in an animal model identifies a novel allosteric regulatory mechanism.

  • Pif1-family helicases cooperatively suppress widespread replication-fork arrest at tRNA genes

  • Genome-wide analyses of S. cerevisiae replisome mobility reveal overlapping roles of Pif1 and Rrm3 helicases in alleviating replication-fork arrest at tRNA genes.

  • Structural basis for targeted DNA cytosine deamination and mutagenesis by APOBEC3A and APOBEC3B

  • Crystal structures of human APOBEC3A and a chimera of APOBEC3B and APOBEC3A bound to ssDNA reveal an unanticipated‘U-shaped’ binding mode and provide insight into target selectivity.

  • Site-specific mapping of the human SUMO proteome reveals co-modification with phosphorylation

  • A comprehensive analysis of the human SUMO proteome, in HeLa and U2OS cell lines and under different conditions, identifies new SUMOylated sites and reveals cross-talk between SUMO and other post-translational modifications, such as phosphorylation.
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