|Entry||Database: EMDB / ID: 3659|
|Title||601 nucleosome in complex with X. laevis histone H1.0b|
|Map data||Nucleosome in complex with X. laevis histone H1.0b|
|Sample||601 nucleosome in complex with X. laevis histone H1.0b:|
|Source||Xenopus laevis (African clawed frog)|
|Method||single particle reconstruction / cryo EM / 11.4 Å resolution|
|Authors||Bednar J / Garcia-Saez I / Boopathi R / Cutter AR / Papai G / Reymer A / Syed SH / Lone IN / Tonchev O / Crucfix C / Menoni H / Papin C / Skoufias DA / Kurumizaka H / Lavery R / Hamiche A / Hayes JJ / Schultz P / Angelov D / Petosa C / Dimitrov S|
|Citation||Journal: Mol. Cell / Year: 2017|
Title: Structure and Dynamics of a 197 bp Nucleosome in Complex with Linker Histone H1.
Authors: Jan Bednar / Isabel Garcia-Saez / Ramachandran Boopathi / Amber R Cutter / Gabor Papai / Anna Reymer / Sajad H Syed / Imtiaz Nisar Lone / Ognyan Tonchev / Corinne Crucifix / Hervé Menoni / Christophe Papin / Dimitrios A Skoufias / Hitoshi Kurumizaka / Richard Lavery / Ali Hamiche / Jeffrey J Hayes / Patrick Schultz / Dimitar Angelov / Carlo Petosa / Stefan Dimitrov
Abstract: Linker histones associate with nucleosomes to promote the formation of higher-order chromatin structure, but the underlying molecular details are unclear. We investigated the structure of a 197 bp ...Linker histones associate with nucleosomes to promote the formation of higher-order chromatin structure, but the underlying molecular details are unclear. We investigated the structure of a 197 bp nucleosome bearing symmetric 25 bp linker DNA arms in complex with vertebrate linker histone H1. We determined electron cryo-microscopy (cryo-EM) and crystal structures of unbound and H1-bound nucleosomes and validated these structures by site-directed protein cross-linking and hydroxyl radical footprinting experiments. Histone H1 shifts the conformational landscape of the nucleosome by drawing the two linkers together and reducing their flexibility. The H1 C-terminal domain (CTD) localizes primarily to a single linker, while the H1 globular domain contacts the nucleosome dyad and both linkers, associating more closely with the CTD-distal linker. These findings reveal that H1 imparts a strong degree of asymmetry to the nucleosome, which is likely to influence the assembly and architecture of higher-order structures.
|Date||Deposition: Apr 4, 2017 / Header (metadata) release: May 17, 2017 / Map release: May 17, 2017 / Last update: Aug 2, 2017|
|Structure viewer||EM map: |
Downloads & links
|File||emd_3659.map.gz (map file in CCP4 format, 30119 KB)|
|Projections & slices|
Images are generated by Spider.
|Voxel size||X=Y=Z: 1.78 Å|
CCP4 map header:
-Entire 601 nucleosome in complex with X. laevis histone H1.0b
|Entire||Name: 601 nucleosome in complex with X. laevis histone H1.0b|
Number of components: 1
-Component #1: protein, 601 nucleosome in complex with X. laevis histone H1.0b
|Protein||Name: 601 nucleosome in complex with X. laevis histone H1.0b|
Recombinant expression: No
|Source||Species: Xenopus laevis (African clawed frog)|
|Source (engineered)||Expression System: Escherichia coli (E. coli)|
|Specimen||Specimen state: particle / Method: cryo EM|
|Sample solution||Specimen conc.: 0.3 mg/ml / pH: 7.2|
|Vitrification||Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 277 K / Humidity: 100 %|
-Electron microscopy imaging
Model: Tecnai Polara / Image courtesy: FEI Company
|Imaging||Microscope: FEI POLARA 300|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 100 kV / Electron dose: 20 e/Å2 / Illumination mode: FLOOD BEAM|
|Lens||Magnification: 59000 X (nominal), 78652 X (calibrated) / Cs: 2 mm / Imaging mode: BRIGHT FIELD|
|Specimen Holder||Model: OTHER|
|Camera||Detector: FEI FALCON I (4k x 4k)|
|Processing||Method: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 5099|
|3D reconstruction||Algorithm: FOURIER SPACE / Software: RELION / Resolution: 11.4 Å / Resolution method: FSC 0.143 CUT-OFF|
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