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Nature Structural & Molecular Biology

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https://www.readbyqxmd.com/read/28414322/parkin-phosphoubiquitin-complex-reveals-cryptic-ubiquitin-binding-site-required-for-rbr-ligase-activity
#1
Atul Kumar, Viduth K Chaugule, Tara E C Condos, Kathryn R Barber, Clare Johnson, Rachel Toth, Ramasubramanian Sundaramoorthy, Axel Knebel, Gary S Shaw, Helen Walden
RING-between-RING (RBR) E3 ligases are a class of ubiquitin ligases distinct from RING or HECT E3 ligases. An important RBR ligase is Parkin, mutations in which lead to early-onset hereditary Parkinsonism. Parkin and other RBR ligases share a catalytic RBR module but are usually autoinhibited and activated via distinct mechanisms. Recent insights into Parkin regulation predict large, unknown conformational changes during Parkin activation. However, current data on active RBR ligases reflect the absence of regulatory domains...
April 17, 2017: Nature Structural & Molecular Biology
https://www.readbyqxmd.com/read/28414321/an-orthogonal-single-molecule-experiment-reveals-multiple-attempt-dynamics-of-type-ia-topoisomerases
#2
Kathryn H Gunn, John F Marko, Alfonso Mondragón
Topoisomerases are enzymes that are involved in maintaining the topological state of cellular DNA. Their dynamic characteristics remain poorly understood despite numerous structural, biophysical and biochemical studies. Recent single-molecule experiments revealed that an important feature of the type IA topoisomerase mechanism is the presence of pauses between relaxation events. However, these experiments could not determine whether the protein remains DNA bound during the pauses or what relationship may exist between protein domain movements and topological changes in the DNA...
April 17, 2017: Nature Structural & Molecular Biology
https://www.readbyqxmd.com/read/28394326/intraflagellar-transport-dynein-is-autoinhibited-by-trapping-of-its-mechanical-and-track-binding-elements
#3
Katerina Toropova, Miroslav Mladenov, Anthony J Roberts
Cilia are multifunctional organelles that are constructed using intraflagellar transport (IFT) of cargo to and from their tip. It is widely held that the retrograde IFT motor, dynein-2, must be controlled in order to reach the ciliary tip and then unleashed to power the return journey. However, the mechanism is unknown. Here, we systematically define the mechanochemistry of human dynein-2 motors as monomers, dimers, and multimotor assemblies with kinesin-II. Combining these data with insights from single-particle EM, we discover that dynein-2 dimers are intrinsically autoinhibited...
April 10, 2017: Nature Structural & Molecular Biology
https://www.readbyqxmd.com/read/28394325/structural-basis-for-lipopolysaccharide-extraction-by-abc-transporter-lptb2fg
#4
Qingshan Luo, Xu Yang, Shan Yu, Huigang Shi, Kun Wang, Le Xiao, Guangyu Zhu, Chuanqi Sun, Tingting Li, Dianfan Li, Xinzheng Zhang, Min Zhou, Yihua Huang
After biosynthesis, bacterial lipopolysaccharides (LPS) are transiently anchored to the outer leaflet of the inner membrane (IM). The ATP-binding cassette (ABC) transporter LptB2FG extracts LPS molecules from the IM and transports them to the outer membrane. Here we report the crystal structure of nucleotide-free LptB2FG from Pseudomonas aeruginosa. The structure reveals that lipopolysaccharide transport proteins LptF and LptG each contain a transmembrane domain (TMD), a periplasmic β-jellyroll-like domain and a coupling helix that interacts with LptB on the cytoplasmic side...
April 10, 2017: Nature Structural & Molecular Biology
https://www.readbyqxmd.com/read/28368393/structure-of-the-40s-abce1-post-splitting-complex-in-ribosome-recycling-and-translation-initiation
#5
André Heuer, Milan Gerovac, Christian Schmidt, Simon Trowitzsch, Anne Preis, Peter Kötter, Otto Berninghausen, Thomas Becker, Roland Beckmann, Robert Tampé
The essential ATP-binding cassette protein ABCE1 splits 80S ribosomes into 60S and 40S subunits after canonical termination or quality-control-based mRNA surveillance processes. However, the underlying splitting mechanism remains enigmatic. Here, we present a cryo-EM structure of the yeast 40S-ABCE1 post-splitting complex at 3.9-Å resolution. Compared to the pre-splitting state, we observe repositioning of ABCE1's iron-sulfur cluster domain, which rotates 150° into a binding pocket on the 40S subunit. This repositioning explains a newly observed anti-association activity of ABCE1...
April 3, 2017: Nature Structural & Molecular Biology
https://www.readbyqxmd.com/read/28346433/a-cytosolic-ezh1-isoform-modulates-a-prc2-ezh1-epigenetic-adaptive-response-in-postmitotic-cells
#6
Beatrice Bodega, Federica Marasca, Valeria Ranzani, Alessandro Cherubini, Francesco Della Valle, Maria Victoria Neguembor, Michel Wassef, Alessio Zippo, Chiara Lanzuolo, Massimiliano Pagani, Valerio Orlando
The evolution of chromatin-based epigenetic cell memory may be driven not only by the necessity for cells to stably maintain transcription programs, but also by the need to recognize signals and allow plastic responses to environmental stimuli. The mechanistic role of the epigenome in adult postmitotic tissues, however, remains largely unknown. In vertebrates, two variants of the Polycomb repressive complex (PRC2-Ezh2 and PRC2-Ezh1) control gene silencing via methylation of histone H3 on Lys27 (H3K27me). Here we describe a reversible mechanism that involves a novel isoform of Ezh1 (Ezh1β)...
March 27, 2017: Nature Structural & Molecular Biology
https://www.readbyqxmd.com/read/28191894/open-ringed-structure-of-the-cdt1-mcm2-7-complex-as-a-precursor-of-the-mcm-double-hexamer
#7
Yuanliang Zhai, Erchao Cheng, Hao Wu, Ningning Li, Philip Yuk Kwong Yung, Ning Gao, Bik-Kwoon Tye
The minichromosome maintenance complex (MCM) hexameric complex (Mcm2-7) forms the core of the eukaryotic replicative helicase. During G1 phase, two Cdt1-Mcm2-7 heptamers are loaded onto each replication origin by the origin-recognition complex (ORC) and Cdc6 to form an inactive MCM double hexamer (DH), but the detailed loading mechanism remains unclear. Here we examine the structures of the yeast MCM hexamer and Cdt1-MCM heptamer from Saccharomyces cerevisiae. Both complexes form left-handed coil structures with a 10-15-Å gap between Mcm5 and Mcm2, and a central channel that is occluded by the C-terminal domain winged-helix motif of Mcm5...
February 13, 2017: Nature Structural & Molecular Biology
https://www.readbyqxmd.com/read/28165511/rdrp-synthesized-antisense-ribosomal-sirnas-silence-pre-rrna-via-the-nuclear-rnai-pathway
#8
Xufei Zhou, Xuezhu Feng, Hui Mao, Mu Li, Fei Xu, Kai Hu, Shouhong Guang
Expression of rRNA affects cell growth and proliferation, but mechanisms that modulate rRNA levels are poorly understood. We conducted a genetic screen for factors that negatively regulate generation of endogenous short interfering RNA (endo-siRNA) in Caenorhabditis elegans and identified a suppressor of siRNA (susi-1) and antisense ribosomal siRNAs (risiRNAs). risiRNAs show sequence complementary to 18S and 26S rRNAs and require RNA-dependent RNA polymerases (RdRPs) for their production. They act through the nuclear RNA interference (RNAi) pathway to downregulate pre-rRNA...
February 6, 2017: Nature Structural & Molecular Biology
https://www.readbyqxmd.com/read/28165509/structural-basis-of-the-specificity-of-usp18-toward-isg15
#9
Anja Basters, Paul P Geurink, Annika Röcker, Katharina F Witting, Roya Tadayon, Sandra Hess, Marta S Semrau, Paola Storici, Huib Ovaa, Klaus-Peter Knobeloch, Günter Fritz
Protein modification by ubiquitin and ubiquitin-like modifiers (Ubls) is counteracted by ubiquitin proteases and Ubl proteases, collectively termed DUBs. In contrast to other proteases of the ubiquitin-specific protease (USP) family, USP18 shows no reactivity toward ubiquitin but specifically deconjugates the interferon-induced Ubl ISG15. To identify the molecular determinants of this specificity, we solved the crystal structures of mouse USP18 alone and in complex with mouse ISG15. USP18 was crystallized in an open and a closed conformation, thus revealing high flexibility of the enzyme...
February 6, 2017: Nature Structural & Molecular Biology
https://www.readbyqxmd.com/read/28134932/eukaryotic-rad50-functions-as-a-rod-shaped-dimer
#10
Young Bong Park, Marcel Hohl, Michał Padjasek, Eunyoung Jeong, Kyeong Sik Jin, Artur Krężel, John H J Petrini, Yunje Cho
The Rad50 hook interface is crucial for assembly and various functions of the Mre11 complex. Previous analyses suggested that Rad50 molecules interact within (intracomplex) or between (intercomplex) dimeric complexes. In this study, we determined the structure of the human Rad50 hook and coiled-coil domains. The data suggest that the predominant structure is the intracomplex, in which the two parallel coiled coils proximal to the hook form a rod shape, and that a novel interface within the coiled-coil domains of Rad50 stabilizes the interaction of Rad50 protomers in the dimeric assembly...
January 30, 2017: Nature Structural & Molecular Biology
https://www.readbyqxmd.com/read/28384136/remodelers-tap-into-nucleosome-plasticity
#11
Hari R Singh, Magdalena Murawska, Andreas G Ladurner
No abstract text is available yet for this article.
April 6, 2017: Nature Structural & Molecular Biology
https://www.readbyqxmd.com/read/28384135/separase-securin-complex-a-cunning-way-to-control-chromosome-segregation
#12
Martin R Singleton, Frank Uhlmann
No abstract text is available yet for this article.
April 6, 2017: Nature Structural & Molecular Biology
https://www.readbyqxmd.com/read/28384134/surveillance-states
#13
Pradyot Dash, Paul G Thomas
No abstract text is available yet for this article.
April 6, 2017: Nature Structural & Molecular Biology
https://www.readbyqxmd.com/read/28319083/structures-of-human-o-glcnacase-and-its-complexes-reveal-a-new-substrate-recognition-mode
#14
Baobin Li, Hao Li, Lei Lu, Jiaoyang Jiang
Human O-GlcNAcase (hOGA) is the unique enzyme responsible for the hydrolysis of the O-linked β-N-acetyl glucosamine (O-GlcNAc) modification, an essential protein glycosylation event that modulates the function of numerous cellular proteins in response to nutrients and stress. Here we report crystal structures of a truncated hOGA, which comprises the catalytic and stalk domains, in apo form, in complex with an inhibitor, and in complex with a glycopeptide substrate. We found that hOGA forms an unusual arm-in-arm homodimer in which the catalytic domain of one monomer is covered by the stalk domain of the sister monomer to create a substrate-binding cleft...
April 2017: Nature Structural & Molecular Biology
https://www.readbyqxmd.com/read/28287632/a-mammalian-nervous-system-specific-plasma-membrane-proteasome-complex-that-modulates-neuronal-function
#15
Kapil V Ramachandran, Seth S Margolis
In the nervous system, rapidly occurring processes such as neuronal transmission and calcium signaling are affected by short-term inhibition of proteasome function. It is unclear how proteasomes are able to acutely regulate such processes, as this action is inconsistent with their canonical role in proteostasis. Here we describe a mammalian nervous-system-specific membrane proteasome complex that directly and rapidly modulates neuronal function by degrading intracellular proteins into extracellular peptides that can stimulate neuronal signaling...
April 2017: Nature Structural & Molecular Biology
https://www.readbyqxmd.com/read/28263325/genome-wide-mapping-of-long-range-contacts-unveils-clustering-of-dna-double-strand-breaks-at-damaged-active-genes
#16
François Aymard, Marion Aguirrebengoa, Emmanuelle Guillou, Biola M Javierre, Beatrix Bugler, Coline Arnould, Vincent Rocher, Jason S Iacovoni, Anna Biernacka, Magdalena Skrzypczak, Krzysztof Ginalski, Maga Rowicka, Peter Fraser, Gaëlle Legube
The ability of DNA double-strand breaks (DSBs) to cluster in mammalian cells has been a subject of intense debate in recent years. Here we used a high-throughput chromosome conformation capture assay (capture Hi-C) to investigate clustering of DSBs induced at defined loci in the human genome. The results unambiguously demonstrated that DSBs cluster, but only when they are induced within transcriptionally active genes. Clustering of damaged genes occurs primarily during the G1 cell-cycle phase and coincides with delayed repair...
April 2017: Nature Structural & Molecular Biology
https://www.readbyqxmd.com/read/28263324/cryo-em-structure-of-a-metazoan-separase-securin-complex-at-near-atomic-resolution
#17
Andreas Boland, Thomas G Martin, Ziguo Zhang, Jing Yang, Xiao-Chen Bai, Leifu Chang, Sjors H W Scheres, David Barford
Separase is a caspase-family protease that initiates chromatid segregation by cleaving the kleisin subunits (Scc1 and Rec8) of cohesin, and regulates centrosome duplication and mitotic spindle function through cleavage of kendrin and Slk19. To understand the mechanisms of securin regulation of separase, we used single-particle cryo-electron microscopy (cryo-EM) to determine a near-atomic-resolution structure of the Caenorhabditis elegans separase-securin complex. Separase adopts a triangular-shaped bilobal architecture comprising an N-terminal tetratricopeptide repeat (TPR)-like α-solenoid domain docked onto the conserved C-terminal protease domain...
April 2017: Nature Structural & Molecular Biology
https://www.readbyqxmd.com/read/28250417/broad-tcr-repertoire-and-diverse-structural-solutions-for-recognition-of-an-immunodominant-cd8-t-cell-epitope
#18
InYoung Song, Anna Gil, Rabinarayan Mishra, Dario Ghersi, Liisa K Selin, Lawrence J Stern
A keystone of antiviral immunity is CD8(+) T cell recognition of viral peptides bound to MHC-I proteins. The recognition modes of individual T cell receptors (TCRs) have been studied in some detail, but the role of TCR variation in providing a robust response to viral antigens is unclear. The influenza M1 epitope is an immunodominant target of CD8(+) T cells that help to control influenza in HLA-A2(+) individuals. Here we show that CD8(+) T cells use many distinct TCRs to recognize HLA-A2-M1, which enables the use of different structural solutions to the problem of specifically recognizing a relatively featureless peptide antigen...
April 2017: Nature Structural & Molecular Biology
https://www.readbyqxmd.com/read/28250416/top2-synergizes-with-baf-chromatin-remodeling-for-both-resolution-and-formation-of-facultative-heterochromatin
#19
Erik L Miller, Diana C Hargreaves, Cigall Kadoch, Chiung-Ying Chang, Joseph P Calarco, Courtney Hodges, Jason D Buenrostro, Kairong Cui, William J Greenleaf, Keji Zhao, Gerald R Crabtree
The resolution and formation of facultative heterochromatin are essential for development, reprogramming, and oncogenesis. The mechanisms underlying these changes are poorly understood owing to the difficulty of studying heterochromatin dynamics and structure in vivo. We devised an in vivo approach to investigate these mechanisms and found that topoisomerase II (TOP2), but not TOP1, synergizes with BAF (mSWI/SNF) ATP-dependent chromatin remodeling complexes genome-wide to resolve facultative heterochromatin to accessible chromatin independent of transcription...
April 2017: Nature Structural & Molecular Biology
https://www.readbyqxmd.com/read/28218750/quaternary-contact-in-the-initial-interaction-of-cd4-with-the-hiv-1-envelope-trimer
#20
Qingbo Liu, Priyamvada Acharya, Michael A Dolan, Peng Zhang, Christina Guzzo, Jacky Lu, Alice Kwon, Deepali Gururani, Huiyi Miao, Tatsiana Bylund, Gwo-Yu Chuang, Aliaksandr Druz, Tongqing Zhou, William J Rice, Christoph Wigge, Bridget Carragher, Clinton S Potter, Peter D Kwong, Paolo Lusso
Binding of the gp120 envelope (Env) glycoprotein to the CD4 receptor is the first step in the HIV-1 infectious cycle. Although the CD4-binding site has been extensively characterized, the initial receptor interaction has been difficult to study because of major CD4-induced structural rearrangements. Here we used cryogenic electron microscopy (cryo-EM) to visualize the initial contact of CD4 with the HIV-1 Env trimer at 6.8-Å resolution. A single CD4 molecule is embraced by a quaternary HIV-1-Env surface formed by coalescence of the previously defined CD4-contact region with a second CD4-binding site (CD4-BS2) in the inner domain of a neighboring gp120 protomer...
April 2017: Nature Structural & Molecular Biology
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