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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

  • Plasmepsin V shows its carnivorous side

  • Export of effector proteins is crucial for the virulence program of the malaria parasite Plasmodium falciparum. A crystal structure of the P. falciparum processing enzyme essential for protein export reveals noncanonical aspartic protease features and provides an avenue for antimalarial drug development.

  • Want reprogramming? Cut back on the chromatin assembly!

  • Totipotency, the ability of early embryonic cells to generate a complete adult organism as well as extraembryonic tissue, is a fleeting property found only in very early embryonic cells. A breakthrough study now shows that inhibition of DNA replication–linked nucleosome assembly causes embryonic stem cells to resemble totipotent cells. Notably, inhibition of chromatin assembly stimulates reprogramming during somatic-cell nuclear transfer experiments.

  • PsbS is the plants' pick for sun protection

  • Plants protect themselves from fluctuating high-light conditions by dissipating a large part of their absorbed energy as heat, in a process that requires the protein PsbS. The structure of PsbS opens new possibilities for understanding the mechanism of photoprotection in plants.

  • A timer to coordinate substrate processing by the 26S proteasome

  • The eukaryotic 26S proteasome is responsible for degrading virtually any protein with an appropriate ubiquitin signal, and in the process ubiquitin is spared and recycled. Two studies of the proteasome-associated deubiquitinase UBP6 now shed light on how deubiquitination coordinates the cycle of substrate processing.

  • SMC condensin: promoting cohesion of replicon arms

  • Two studies using chromosome conformation capture (3C) analyses in the Gram-positive bacterium Bacillus subtilis have revealed a global pattern of chromosome organization that originates from loading sites of the Smc–ScpAB complex. Loading Smc–ScpAB at a single genomic location is sufficient to promote genome-wide folding of DNA into a well-defined structure.

  • PAR and the organization of the DNA damage response

  • Charting oxidized methylcytosines at base resolution

  • New methods permit genomic mapping of oxidized methylcytosines at single-base resolution and suggest new regulatory functions for 5-methylcytocine (5mC) derivatives 5hmC, 5fC and 5caC in the mammalian genome.

  • Early embryonic-like cells are induced by downregulating replication-dependent chromatin assembly

  • New data show that depletion of histone chaperone CAF-1 in mouse embryonic stem (ES) cells induces early embryonic-like cells that exhibit gene-expression patterns and reprogramming efficiencies characteristic of 2-cell-stage populations that arise spontaneously in ES-cell culture, thus suggesting that altered chromatin assembly contributes to differences in stem-cell plasticity.

  • The tuberculosis necrotizing toxin kills macrophages by hydrolyzing NAD

  • The Mycobacterium tuberculosis necrotizing toxin (TNT) is shown to cause toxicity by hydrolyzing NAD+ in the host cell. The crystal structure of TNT bound to its immunity factor reveals a new NAD+ glycohydrolase fold.

  • Recognition of the bacterial alarmone ZMP through long-distance association of two RNA subdomains

  • The cocrystal structure of bacterial alarmone ZMP with its cognate riboswitch reveals how the two subdomains of the latter mediate ligand recognition. Supporting biochemical analyses show that ligand binding affinity and transcription antitermination are modulated by the interdomain linker length.

  • Probing Gαi1 protein activation at single–amino acid resolution

  • Extensive mutant cycle analysis provides a map of the residues that contribute to stability and activation-associated conformational dynamics of the Gαi1 protein in nucleotide-bound states and in complex with the G protein–coupled receptor rhodopsin.

  • Structure of Rab11–FIP3–Rabin8 reveals simultaneous binding of FIP3 and Rabin8 effectors to Rab11

  • Dual effector binding to the small GTPase Rab11 suggests that membrane-targeting complexes involved in vesicular transport might assemble through multiple weak interactions to create high-avidity assemblies.

  • Structure and mechanism of activity-based inhibition of the EGF receptor by Mig6

  • Mig6 phosphorylation at two consecutive tyrosines induces rearrangements that lead to Mig6 sticking to and inhibiting the same EGFR that catalyzed its phosphorylation. This mechanism may serve as a basis for inhibition of oncogenic EGFR variants.

  • Ubp6 deubiquitinase controls conformational dynamics and substrate degradation of the 26S proteasome

  • Electron microscopy and biochemistry analyses reveal that the deubiquitinase Ubp6, in its ubiquitin-bound form, inhibits substrate deubiquitination by Rpn11, stabilizes the proteasome in a substrate-engaged conformation and interferes with the engagement of a subsequent substrate.

  • Structure and mechanism of the Rubisco-assembly chaperone Raf1

  • Biochemical and structural analyses show that Rubisco accumulation factor 1 (Raf1) stabilizes RbcL dimers, which then assemble into octamers. Raf1 is then displaced by RbcS, thus yielding the Rubisco holoenzyme.

  • Crystal structures of the PsbS protein essential for photoprotection in plants

  • PsbS is a transmembrane photosystem II protein essential for photoprotection in plants. Crystal structures show that PsbS is not a canonical pigment-binding protein and provide insights into its pH-dependent activation mechanism.

  • Recruitment and activation of the ATM kinase in the absence of DNA-damage sensors

  • The ATM kinase is shown to be recruited to sites of DNA damage, where it phosphorylates H2AX and triggers the G2-M checkpoint, in the absence of both MRN and Ku70–Ku80.

  • The active site of O-GlcNAc transferase imposes constraints on substrate sequence

  • O-GlcNAcylation is a post-translational modification catalyzed by O-GlcNAc transferase. Here, a high-throughput activity assay combined with mass spectrometric and crystallographic analyses sheds light on the substrate recognition and specificity of O-GlcNAc transferase.

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    Nature -Advance Online Publications

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

  • Structural basis for specific recognition of single-stranded RNA by Toll-like receptor 13

  • Crystallographic and cryo-EM analyses of short synthetic single-stranded RNA–bound peptides unveil the structural basis for recognition of bacterial 23S rRNA and vesicular stomatitis virus by Toll-like receptor 13, which triggers an immune response.

  • Histone monoubiquitination by Clock–Bmal1 complex marks Per1 and Per2 genes for circadian feedback

  • New data show that Clock–Bmal1, the central transcriptional activator that drives expression of circadian target genes, also recruits the Ddb1–Cullin-4 ubiquitin ligase to clock promoters to enhance the subsequent binding of the feedback repressors that generate the circadian periodicity of gene expression.

  • Ubp6 deubiquitinase controls conformational dynamics and substrate degradation of the 26S proteasome

  • Electron microscopy and biochemistry analyses reveal that the deubiquitinase Ubp6, in its ubiquitin-bound form, inhibits substrate deubiquitination by Rpn11, stabilizes the proteasome in a substrate-engaged conformation and interferes with the engagement of a subsequent substrate.

  • Recruitment and activation of the ATM kinase in the absence of DNA-damage sensors

  • The ATM kinase is shown to be recruited to sites of DNA damage, where it phosphorylates H2AX and triggers the G2-M checkpoint, in the absence of both MRN and Ku70–Ku80.

  • Recognition of the bacterial alarmone ZMP through long-distance association of two RNA subdomains

  • The cocrystal structure of bacterial alarmone ZMP with its cognate riboswitch reveals how the two subdomains of the latter mediate ligand recognition. Supporting biochemical analyses show that ligand binding affinity and transcription antitermination are modulated by the interdomain linker length.

  • Structure and mechanism of activity-based inhibition of the EGF receptor by Mig6

  • Mig6 phosphorylation at two consecutive tyrosines induces rearrangements that lead to Mig6 sticking to and inhibiting the same EGFR that catalyzed its phosphorylation. This mechanism may serve as a basis for inhibition of oncogenic EGFR variants.

  • Crystal structures of the PsbS protein essential for photoprotection in plants

  • PsbS is a transmembrane photosystem II protein essential for photoprotection in plants. Crystal structures show that PsbS is not a canonical pigment-binding protein and provide insights into its pH-dependent activation mechanism.

  • Probing Gαi1 protein activation at single–amino acid resolution

  • Extensive mutant cycle analysis provides a map of the residues that contribute to stability and activation-associated conformational dynamics of the Gαi1 protein in nucleotide-bound states and in complex with the G protein–coupled receptor rhodopsin.

  • Structure of Rab11–FIP3–Rabin8 reveals simultaneous binding of FIP3 and Rabin8 effectors to Rab11

  • Dual effector binding to the small GTPase Rab11 suggests that membrane-targeting complexes involved in vesicular transport might assemble through multiple weak interactions to create high-avidity assemblies.

  • Structure and mechanism of the Rubisco-assembly chaperone Raf1

  • Biochemical and structural analyses show that Rubisco accumulation factor 1 (Raf1) stabilizes RbcL dimers, which then assemble into octamers. Raf1 is then displaced by RbcS, thus yielding the Rubisco holoenzyme.

  • Early embryonic-like cells are induced by downregulating replication-dependent chromatin assembly

  • New data show that depletion of histone chaperone CAF-1 in mouse embryonic stem (ES) cells induces early embryonic-like cells that exhibit gene-expression patterns and reprogramming efficiencies characteristic of 2-cell-stage populations that arise spontaneously in ES-cell culture, thus suggesting that altered chromatin assembly contributes to differences in stem-cell plasticity.

  • The active site of O-GlcNAc transferase imposes constraints on substrate sequence

  • O-GlcNAcylation is a post-translational modification catalyzed by O-GlcNAc transferase. Here, a high-throughput activity assay combined with mass spectrometric and crystallographic analyses sheds light on the substrate recognition and specificity of O-GlcNAc transferase.

  • The tuberculosis necrotizing toxin kills macrophages by hydrolyzing NAD

  • The Mycobacterium tuberculosis necrotizing toxin (TNT) is shown to cause toxicity by hydrolyzing NAD+ in the host cell. The crystal structure of TNT bound to its immunity factor reveals a new NAD+ glycohydrolase fold.
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