scholarly journals Structural basis for 5′-end-specific recognition of guide RNA by the A. fulgidus Piwi protein

Nature ◽  
2005 ◽  
Vol 434 (7033) ◽  
pp. 666-670 ◽  
Author(s):  
Jin-Biao Ma ◽  
Yu-Ren Yuan ◽  
Gunter Meister ◽  
Yi Pei ◽  
Thomas Tuschl ◽  
...  
Keyword(s):  
Structural Basis ◽  
Piwi Protein ◽  
Guide Rna ◽  
Specific Recognition

Structural basis for 5′-nucleotide base-specific recognition of guide RNA by human AGO2

Nature ◽  
2010 ◽  
Vol 465 (7299) ◽  
pp. 818-822 ◽  
Author(s):  
Filipp Frank ◽  
Nahum Sonenberg ◽  
Bhushan Nagar
Keyword(s):  
Structural Basis ◽  
Guide Rna ◽  
Specific Recognition ◽  
Nucleotide Base

scholarly journals Structural Basis for the Specific Recognition of RET by the Dok1 Phosphotyrosine Binding Domain

2003 ◽  
Vol 279 (6) ◽  
pp. 4962-4969 ◽  
Author(s):  
Ning Shi ◽  
Sheng Ye ◽  
Mark Bartlam ◽  
Maojun Yang ◽  
Jing Wu ◽  
...  
Keyword(s):  
Binding Domain ◽  
Structural Basis ◽  
Specific Recognition ◽  
Phosphotyrosine Binding Domain

scholarly journals Mechanism of R-loop formation and conformational activation of Cas9

2021 ◽  
Author(s):  
Martin Pacesa ◽  
Martin Jinek
Keyword(s):  
Dna Cleavage ◽  
Structural Basis ◽  
Seed Region ◽  
Loop Formation ◽  
Base Pairs ◽  
Guide Rna ◽  
Target Strand ◽  
Target Dna ◽  
Dna Strand ◽  
Dna Substrate

Cas9 is a CRISPR-associated endonuclease capable of RNA-guided, site-specific DNA cleavage. The programmable activity of Cas9 has been widely utilized for genome editing applications. Despite extensive studies, the precise mechanism of target DNA binding and on-/off-target discrimination remains incompletely understood. Here we report cryo-EM structures of intermediate binding states of Streptococcus pyogenes Cas9 that reveal domain rearrangements induced by R-loop propagation and PAM-distal duplex positioning. At early stages of binding, the Cas9 REC2 and REC3 domains form a positively charged cleft that accommodates the PAM-distal duplex of the DNA substrate. Target hybridisation past the seed region positions the guide-target heteroduplex into the central binding channel and results in a conformational rearrangement of the REC lobe. Extension of the R-loop to 16 base pairs triggers the relocation of the HNH domain towards the target DNA strand in a catalytically incompetent conformation. The structures indicate that incomplete target strand pairing fails to induce the conformational displacements necessary for nuclease domain activation. Our results establish a structural basis for target DNA-dependent activation of Cas9 that advances our understanding of its off-target activity and will facilitate the development of novel Cas9 variants and guide RNA designs with enhanced specificity and activity.

Orexin-A is composed of a highly conservedC-terminal and a specific, hydrophilicN-terminal region, revealing the structural basis of specific recognition by the orexin-1 receptor

2006 ◽  
Vol 12 (7) ◽  
pp. 443-454 ◽  
Author(s):  
Tomoyo Takai ◽  
Takao Takaya ◽  
Mutsuko Nakano ◽  
Hideo Akutsu ◽  
Atsushi Nakagawa ◽  
...  
Keyword(s):  
Terminal Region ◽  
Structural Basis ◽  
Orexin A ◽  
Specific Recognition

scholarly journals Structural Basis for Specific Recognition of Reelin by Its Receptors

Structure ◽  
2010 ◽  
Vol 18 (3) ◽  
pp. 320-331 ◽  
Author(s):  
Norihisa Yasui ◽  
Terukazu Nogi ◽  
Junichi Takagi
Keyword(s):  
Structural Basis ◽  
Specific Recognition

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

2015 ◽  
Vol 22 (10) ◽  
pp. 782-787 ◽  
Author(s):  
Wen Song ◽  
Jia Wang ◽  
Zhifu Han ◽  
Yifan Zhang ◽  
Heqiao Zhang ◽  
...  
Keyword(s):  
Structural Basis ◽  
Toll Like Receptor ◽  
Specific Recognition

scholarly journals Structural Basis for Sequence-Specific Recognition of DNA by TAL Effectors

Science ◽  
2012 ◽  
Vol 335 (6069) ◽  
pp. 720-723 ◽  
Author(s):  
D. Deng ◽  
C. Yan ◽  
X. Pan ◽  
M. Mahfouz ◽  
J. Wang ◽  
...  
Keyword(s):  
Structural Basis ◽  
Tal Effectors ◽  
Specific Recognition

scholarly journals Structural basis of ClpXP recognition and unfolding of ssrA-tagged substrates

2020 ◽  
Author(s):  
Xue Fei ◽  
Tristan A Bell ◽  
Sarah R Barkow ◽  
Tania A Baker ◽  
Robert T Sauer
Keyword(s):  
Open Channel ◽  
Structural Basis ◽  
Closed Channel ◽  
E Coli ◽  
Protein Substrates ◽  
Specific Recognition ◽  
Axial Channel ◽  
Engagement Strategies ◽  
C Terminus ◽  
Protein Remodeling

ABSTRACTWhen ribosomes fail to complete normal translation, all cells have mechanisms to ensure degradation of the resulting partial proteins to safeguard proteome integrity. In E. coli and other eubacteria, the tmRNA system rescues stalled ribosomes and adds an ssrA tag or degron to the C-terminus of the incomplete protein, which directs degradation by the AAA+ ClpXP protease. Here, we present cryo-EM structures of ClpXP bound to the ssrA degron. C-terminal residues of the ssrA degron initially bind in the top of an otherwise closed ClpX axial channel and subsequently move deeper into an open channel. For short-degron protein substrates, we show that unfolding can occur directly from the initial closed-channel complex. For longer-degron substrates, our studies illuminate how ClpXP transitions from specific recognition into a nonspecific unfolding and translocation machine. Many AAA+ proteases and protein-remodeling motors are likely to employ similar multistep recognition and engagement strategies.

scholarly journals Structural basis for the specific recognition of DSR by the YTH domain containing protein Mmi1

2017 ◽  
Author(s):  
Baixing Wu ◽  
Jinhao Xu ◽  
Shichen Su ◽  
Hehua Liu ◽  
Jianhua Gan ◽  
...  
Keyword(s):  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Mitotic Cell ◽  
Structural Basis ◽  
Core Motif ◽  
Specific Recognition ◽  
Specific Mrnas ◽  
Striking Change ◽  
Yth Domain ◽  
Mitotic Cells

AbstractMeiosis is one of the most dramatic differentiation programs accompanied by a striking change in gene expression profiles, whereas a number of meiosis-specific transcripts are expressed untimely in mitotic cells. The entry of meiosis will be blocked as the accumulation of meiosis-specific mRNAs during the mitotic cell in fission yeast Schizosaccharomyces pombe. A YTH domain containing protein Mmi1 was identified as a pivotal effector in a post-transcriptional event termed selective elimination of meiosis-specific mRNAs, Mmi1 can recognize and bind a class of meiosis-specific transcripts expressed inappropriately in mitotic cells, which contain a conservative motif called DSR as a mark to remove them in cooperation with nuclear exosomes. Here we report the 1.6 Å resolution crystal structure of the YTH domain of Mmi1 binds to high-affinity RNA targets r(A1U2U3A4A5A6C7A8) containing DSR core motif. Our structure observations, supported by site-directed mutations of key residues illustrate the mechanism for specific recognition of DSR-RNA by Mmi1. Moreover, different from other YTH domain family proteins, Mmi1 YTH domain has a distinctive function although it has a similar fold as other ones.

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