Cryo-EM structure of the human cohesin-NIPBL-DNA complex

Science ◽  
2020 ◽  
Vol 368 (6498) ◽  
pp. 1454-1459 ◽  
Author(s):  
Zhubing Shi ◽  
Haishan Gao ◽  
Xiao-chen Bai ◽  
Hongtao Yu
Keyword(s):  
Electron Microscopy ◽  
Sister Chromatid ◽  
Base Pair ◽  
Adenosine Triphosphatase ◽  
Cryo Electron Microscopy ◽  
Synergistic Activation ◽  
Medium Resolution ◽  
Chromatid Cohesion ◽  
Dna Complex ◽  
Insight Into

As a ring-shaped adenosine triphosphatase (ATPase) machine, cohesin organizes the eukaryotic genome by extruding DNA loops and mediates sister chromatid cohesion by topologically entrapping DNA. How cohesin executes these fundamental DNA transactions is not understood. Using cryo–electron microscopy (cryo-EM), we determined the structure of human cohesin bound to its loader NIPBL and DNA at medium resolution. Cohesin and NIPBL interact extensively and together form a central tunnel to entrap a 72–base pair DNA. NIPBL and DNA promote the engagement of cohesin’s ATPase head domains and ATP binding. The hinge domains of cohesin adopt an “open washer” conformation and dock onto the STAG1 subunit. Our structure explains the synergistic activation of cohesin by NIPBL and DNA and provides insight into DNA entrapment by cohesin.

scholarly journals Cylindrical Similarity Measurement for Helices in Medium-Resolution Cryo-Electron Microscopy Density Maps

2020 ◽  
Vol 60 (5) ◽  
pp. 2644-2650 ◽  
Author(s):  
Salim Sazzed ◽  
Peter Scheible ◽  
Maytha Alshammari ◽  
Willy Wriggers ◽  
Jing He
Keyword(s):  
Electron Microscopy ◽  
Similarity Measurement ◽  
Cryo Electron Microscopy ◽  
Density Maps ◽  
Medium Resolution

scholarly journals The Combination of X-Ray Crystallography and Cryo-Electron Microscopy Provides Insight into the Overall Architecture of the Dodecameric Rvb1/Rvb2 Complex

PLoS ONE ◽  
2016 ◽  
Vol 11 (1) ◽  
pp. e0146457 ◽  
Author(s):  
Noella Silva-Martin ◽  
María I. Daudén ◽  
Sebastian Glatt ◽  
Niklas A. Hoffmann ◽  
Panagiotis Kastritis ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
X Ray ◽  
X Ray Crystallography ◽  
Cryo Electron Microscopy ◽  
Insight Into

Structural insight into nucleosome transcription by RNA polymerase II with elongation factors

Science ◽  
2019 ◽  
Vol 363 (6428) ◽  
pp. 744-747 ◽  
Author(s):  
Haruhiko Ehara ◽  
Tomoya Kujirai ◽  
Yuka Fujino ◽  
Mikako Shirouzu ◽  
Hitoshi Kurumizaka ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Transcription Elongation ◽  
Chromosomal Dna ◽  
Elongation Factors ◽  
Cryo Electron Microscopy ◽  
Structural Insight ◽  
Insight Into

RNA polymerase II (RNAPII) transcribes chromosomal DNA that contains multiple nucleosomes. The nucleosome forms transcriptional barriers, and nucleosomal transcription requires several additional factors in vivo. We demonstrate that the transcription elongation factors Elf1 and Spt4/5 cooperatively lower the barriers and increase the RNAPII processivity in the nucleosome. The cryo–electron microscopy structures of the nucleosome-transcribing RNAPII elongation complexes (ECs) reveal that Elf1 and Spt4/5 reshape the EC downstream edge and intervene between RNAPII and the nucleosome. They facilitate RNAPII progression through superhelical location SHL(–1) by adjusting the nucleosome in favor of the forward progression. They suppress pausing at SHL(–5) by preventing the stable RNAPII-nucleosome interaction. Thus, the EC overcomes the nucleosomal barriers while providing a platform for various chromatin functions.

scholarly journals Template-free 13-protofilament microtubule–MAP assembly visualized at 8 Å resolution

2010 ◽  
Vol 191 (3) ◽  
pp. 463-470 ◽  
Author(s):  
Franck J. Fourniol ◽  
Charles V. Sindelar ◽  
Béatrice Amigues ◽  
Daniel K. Clare ◽  
Geraint Thomas ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Structural Information ◽  
Binding Mode ◽  
Microtubule Associated Proteins ◽  
Cryo Electron Microscopy ◽  
Associated Proteins ◽  
Template Free ◽  
Map Function ◽  
Insight Into

Microtubule-associated proteins (MAPs) are essential for regulating and organizing cellular microtubules (MTs). However, our mechanistic understanding of MAP function is limited by a lack of detailed structural information. Using cryo-electron microscopy and single particle algorithms, we solved the 8 Å structure of doublecortin (DCX)-stabilized MTs. Because of DCX’s unusual ability to specifically nucleate and stabilize 13-protofilament MTs, our reconstruction provides unprecedented insight into the structure of MTs with an in vivo architecture, and in the absence of a stabilizing drug. DCX specifically recognizes the corner of four tubulin dimers, a binding mode ideally suited to stabilizing both lateral and longitudinal lattice contacts. A striking consequence of this is that DCX does not bind the MT seam. DCX binding on the MT surface indirectly stabilizes conserved tubulin–tubulin lateral contacts in the MT lumen, operating independently of the nucleotide bound to tubulin. DCX’s exquisite binding selectivity uncovers important insights into regulation of cellular MTs.

scholarly journals Structure of the RSC complex bound to the nucleosome

Science ◽  
2019 ◽  
Vol 366 (6467) ◽  
pp. 838-843 ◽  
Author(s):  
Youpi Ye ◽  
Hao Wu ◽  
Kangjing Chen ◽  
Cedric R. Clapier ◽  
Naveen Verma ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Gene Transcription ◽  
Chromatin Structure ◽  
Adenosine Triphosphatase ◽  
Related Protein ◽  
Dna Translocation ◽  
Auxiliary Subunit ◽  
Cryo Electron Microscopy ◽  
Rsc Complex ◽  
Shed Light

The RSC complex remodels chromatin structure and regulates gene transcription. We used cryo–electron microscopy to determine the structure of yeast RSC bound to the nucleosome. RSC is delineated into the adenosine triphosphatase motor, the actin-related protein module, and the substrate recruitment module (SRM). RSC binds the nucleosome mainly through the motor, with the auxiliary subunit Sfh1 engaging the H2A-H2B acidic patch to enable nucleosome ejection. SRM is organized into three substrate-binding lobes poised to bind their respective nucleosomal epitopes. The relative orientations of the SRM and the motor on the nucleosome explain the directionality of DNA translocation and promoter nucleosome repositioning by RSC. Our findings shed light on RSC assembly and functionality, and they provide a framework to understand the mammalian homologs BAF/PBAF and the Sfh1 ortholog INI1/BAF47, which are frequently mutated in cancers.

scholarly journals Hsp90 Is Essential for Chl1-Mediated Chromosome Segregation and Sister Chromatid Cohesion

mSphere ◽  
2018 ◽  
Vol 3 (3) ◽  
Author(s):  
Nidhi Khurana ◽  
Sayan Bakshi ◽  
Wahida Tabassum ◽  
Mrinal K. Bhattacharyya ◽  
Sunanda Bhattacharyya
Keyword(s):  
Sister Chromatid ◽  
Hsp90 Inhibitor ◽  
Sister Chromatid Cohesion ◽  
Chromosome Loss ◽  
Temperature Sensitive ◽  
Restrictive Temperature ◽  
Functional Loss ◽  
Mechanistic Insight ◽  
Chromatid Cohesion ◽  
Insight Into

ABSTRACT Recent studies have demonstrated that aberrant sister chromatid cohesion causes genomic instability and hence is responsible for the development of a tumor. The Chl1 (chromosome loss 1) protein (homolog of human ChlRl/DDX11 helicase) plays an essential role in the proper segregation of chromosomes during mitosis. The helicase activity of Chl1 is critical for sister chromatid cohesion. Our study demonstrates that Hsp90 interacts with Chl1 and is necessary for its stability. We observe that the Hsp90 nonfunctional condition (temperature-sensitive iG170Dhsp82 strain at restrictive temperature) induces proteasomal degradation of Chl1. We have mapped the domains of Chl1 and identified that the presence of domains II, III, and IV is essential for efficient interaction with Hsp90. We have demonstrated that Hsp90 inhibitor 17-AAG (17-allylamino-geldenamycin) causes destabilization of Chl1 protein and enhances significant disruption of sister chromatid cohesion, which is comparable to that observed under the Δchl1 condition. Our study also revealed that 17-AAG treatment causes an increased frequency of chromosome loss to a similar extent as that of the Δchl1 cells. Hsp90 functional loss has been earlier linked to aneuploidy with very poor mechanistic insight. Our result identifies Chl1 as a novel client of Hsp90, which could be further explored to gain mechanistic insight into aneuploidy. IMPORTANCE Recently, Hsp90 functional loss has been linked to aneuploidy; however, until now none of the components of sister chromatid cohesion (SCC) have been demonstrated as the putative clients of Hsp90. In this study, we have established that Chl1, the protein which is involved in maintaining sister chromatid cohesion as well as in preventing chromosome loss, is a direct client of Hsp90. Thus, with understanding of the molecular mechanism, how Hsp90 controls the cohesion machinery might reveal new insights which can be exploited further for attenuation of tumorigenesis.

scholarly journals Cryo-EM structures of the Caspase activated protein XKR9 involved in apoptotic lipid scrambling

2021 ◽  
Author(s):  
Raimund Dutzler ◽  
Monique S. Straub ◽  
Carolina Alvadia ◽  
Marta Sawicka
Keyword(s):  
Electron Microscopy ◽  
Cell Surface ◽  
Protein Function ◽  
Caspase 3 ◽  
Full Length ◽  
Cryo Electron Microscopy ◽  
C Terminus ◽  
Hydrophobic Site ◽  
Membrane Spanning ◽  
Insight Into

The exposure of the negatively charged lipid phosphatidylserine on the cell-surface, catalyzed by lipid scramblases, is an important signal for the clearance of apoptotic cells by macrophages. The protein XKR9 is a member of a conserved family that has been associated with apoptotic lipid scrambling. Here, we describe structures of full-length and caspase-treated XKR9 in complex with a synthetic nanobody determined by cryo-electron microscopy. The 43 kDa monomeric membrane protein contains eight membrane-spanning helices, two segments that are partly inserted into the lipid bilayer and is organized as two structurally related repeats. In the full-length protein, the C-terminus interacts with a hydrophobic site located at the intracellular side acting as an inhibitor of protein function. Cleavage by caspase-3 at a specific site releases 16 residues of the C-terminus thus making the binding site accessible to the cytoplasm. Collectively, the work has revealed the unknown architecture of the XKR family and has provided initial insight into its activation by caspases.

scholarly journals The cohesion protein ORD is required for homologue bias during meiotic recombination

2004 ◽  
Vol 164 (6) ◽  
pp. 819-829 ◽  
Author(s):  
Hayley A. Webber ◽  
Louisa Howard ◽  
Sharon E. Bickel
Keyword(s):  
Electron Microscopy ◽  
Homologous Recombination ◽  
Sister Chromatid ◽  
Meiotic Recombination ◽  
Sister Chromatid Exchange ◽  
Ring Chromosome ◽  
Double Strand Breaks ◽  
Wild Type ◽  
Strand Breaks ◽  
Chromatid Cohesion

During meiosis, sister chromatid cohesion is required for normal levels of homologous recombination, although how cohesion regulates exchange is not understood. Null mutations in orientation disruptor (ord) ablate arm and centromeric cohesion during Drosophila meiosis and severely reduce homologous crossovers in mutant oocytes. We show that ORD protein localizes along oocyte chromosomes during the stages in which recombination occurs. Although synaptonemal complex (SC) components initially associate with synapsed homologues in ord mutants, their localization is severely disrupted during pachytene progression, and normal tripartite SC is not visible by electron microscopy. In ord germaria, meiotic double strand breaks appear and disappear with frequency and timing indistinguishable from wild type. However, Ring chromosome recovery is dramatically reduced in ord oocytes compared with wild type, which is consistent with the model that defects in meiotic cohesion remove the constraints that normally limit recombination between sisters. We conclude that ORD activity suppresses sister chromatid exchange and stimulates inter-homologue crossovers, thereby promoting homologue bias during meiotic recombination in Drosophila.

Sign in / Sign up

Export Citation Format

Share Document