scholarly journals 3.9 Å structure of the nucleosome core particle determined by phase-plate cryo-EM

2016 ◽  
Vol 44 (17) ◽  
pp. 8013-8019 ◽  
Author(s):  
Eugene Y.D. Chua ◽  
Vinod K. Vogirala ◽  
Oviya Inian ◽  
Andrew S.W. Wong ◽  
Lars Nordenskiöld ◽  
...  
Keyword(s):  
Phase Plate ◽  
Core Particle ◽  
Nucleosome Core Particle ◽  
Nucleosome Core

scholarly journals 3.9 Å phase plate cryo-EM reconstruction of the nucleosome core particle

2017 ◽  
Vol 73 (a2) ◽  
pp. C1293-C1293
Author(s):  
Sara Helena Ruth Engholmen Sandin ◽  
Vinod K. Vogirala ◽  
Oviya Inian ◽  
Andrew S. W. Wong ◽  
Lars Nordenskiold ◽  
...  
Keyword(s):  
Phase Plate ◽  
Core Particle ◽  
Nucleosome Core Particle ◽  
Nucleosome Core

scholarly journals Phase-plate cryo-EM structure of the Widom 601 CENP-A nucleosome core particle reveals differential flexibility of the DNA ends

2020 ◽  
Vol 48 (10) ◽  
pp. 5735-5748 ◽  
Author(s):  
Ramachandran Boopathi ◽  
Radostin Danev ◽  
Maryam Khoshouei ◽  
Seyit Kale ◽  
Sunil Nahata ◽  
...  
Keyword(s):  
Image Data ◽  
Dynamics Simulation ◽  
Phase Plate ◽  
Dependent Manner ◽  
Core Particle ◽  
Dynamic Features ◽  
Nucleosome Core Particle ◽  
Nucleosome Core ◽  
Sequence Dependent ◽  
Dna Ends

Abstract The histone H3 variant CENP-A marks centromeres epigenetically and is essential for mitotic fidelity. Previous crystallographic studies of the CENP-A nucleosome core particle (NCP) reconstituted with a human α-satellite DNA derivative revealed both DNA ends to be highly flexible, a feature important for CENP-A mitotic functions. However, recent cryo-EM studies of CENP-A NCP complexes comprising primarily Widom 601 DNA reported well-ordered DNA ends. Here, we report the cryo-EM structure of the CENP-A 601 NCP determined by Volta phase-plate imaging. The data reveal that one (‘left’) 601 DNA end is well ordered whereas the other (‘right’) end is flexible and partly detached from the histone core, suggesting sequence-dependent dynamics of the DNA termini. Indeed, a molecular dynamics simulation of the CENP-A 601 NCP confirmed the distinct dynamics of the two DNA extremities. Reprocessing the image data using two-fold symmetry yielded a cryo-EM map in which both DNA ends appeared well ordered, indicating that such an artefact may inadvertently arise if NCP asymmetry is lost during image processing. These findings enhance our understanding of the dynamic features that discriminate CENP-A from H3 nucleosomes by revealing that DNA end flexibility can be fine-tuned in a sequence-dependent manner.

scholarly journals Structure of the yeast nucleosome core particle reveals fundamental changes in internucleosome interactions

2001 ◽  
Vol 20 (18) ◽  
pp. 5207-5218 ◽  
Author(s):  
Cindy L. White ◽  
Robert K. Suto ◽  
Karolin Luger
Keyword(s):  
Core Particle ◽  
Nucleosome Core Particle ◽  
Nucleosome Core

Helical repeat of DNA in the nucleosome core particle

2000 ◽  
Vol 28 (4) ◽  
pp. 373-376 ◽  
Author(s):  
R. Negri ◽  
M. Buttinelli ◽  
G. Panetta ◽  
V. De Arcangelis ◽  
E. Di Mauro ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Linker Histone ◽  
Core Particle ◽  
Nucleosome Core Particle ◽  
Apparent Paradox ◽  
Nucleosome Core ◽  
Nucleosome Core Particles ◽  
High Affinity Site ◽  
Hydroxyl Radical Cleavage ◽  
Radical Cleavage

Although the crystal structure of nucleosome core particle is essentially symmetrical in the vicinity of the dyad, the linker histone binds asymmetrically in this region to select a single high-affinity site from potentially two equivalent sites. To try to resolve this apparent paradox we mapped to base-pair resolution the dyads and rotational settings of nucleosome core particles reassembled on synthetic tandemly repeating 20 bp DNA sequences. In agreement with previous observations, we observed (1) that the helical repeat on each side of the dyad cluster is 10 bp maintaining register with the sequence repeat and (2) that this register changes by 2 bp in the vicinity of the dyad. The additional 2 bp required to effect the change in the rotational settings is accommodated by an adjustment immediately adjacent to the dyad. At the dyad the hydroxyl radical cleavage is asymmetric and we suggest that the inferred structural asymmetry could direct the binding of the linker histone to a single preferred site.

The Crystal Structure of the Nucleosome Core Particle by Contrast Variation

1984 ◽  
pp. 105-117
Author(s):  
Graham A. Bentley ◽  
John T. Finch ◽  
Anita Lewit-Bentley ◽  
Michel Roth
Keyword(s):  
Crystal Structure ◽  
Core Particle ◽  
Nucleosome Core Particle ◽  
Contrast Variation ◽  
Nucleosome Core
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