+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-3659 | |||||||||
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Title | 601 nucleosome in complex with X. laevis histone H1.0b | |||||||||
Map data | Nucleosome in complex with X. laevis histone H1.0b | |||||||||
Sample |
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Biological species | Xenopus laevis (African clawed frog) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 11.4 Å | |||||||||
Authors | Bednar J / Garcia-Saez I / Boopathi R / Cutter AR / Papai G / Reymer A / Syed SH / Lone IN / Tonchev O / Crucfix C ...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 / ...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. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_3659.map.gz | 2 MB | EMDB map data format | |
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Header (meta data) | emd-3659-v30.xml emd-3659.xml | 12.2 KB 12.2 KB | Display Display | EMDB header |
Images | emd_3659.png | 88.2 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-3659 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-3659 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_3659.map.gz / Format: CCP4 / Size: 28.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Nucleosome in complex with X. laevis histone H1.0b | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.78 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : 601 nucleosome in complex with X. laevis histone H1.0b
Entire | Name: 601 nucleosome in complex with X. laevis histone H1.0b |
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Components |
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-Supramolecule #1: 601 nucleosome in complex with X. laevis histone H1.0b
Supramolecule | Name: 601 nucleosome in complex with X. laevis histone H1.0b type: complex / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Xenopus laevis (African clawed frog) |
Recombinant expression | Organism: Escherichia coli (E. coli) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.3 mg/mL |
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Buffer | pH: 7.2 |
Grid | Model: Quantifoil R2/2 / Material: COPPER/RHODIUM / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI POLARA 300 |
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Electron beam | Acceleration voltage: 100 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 78652 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.0 mm / Nominal magnification: 59000 |
Sample stage | Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: FEI FALCON I (4k x 4k) / Average exposure time: 1.0 sec. / Average electron dose: 20.0 e/Å2 |
Experimental equipment | Model: Tecnai Polara / Image courtesy: FEI Company |
-Image processing
Particle selection | Number selected: 84530 |
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CTF correction | Software - Name: CTFFIND (ver. 3) |
Initial angle assignment | Type: PROJECTION MATCHING / Software - Name: RELION (ver. 1.3) |
Final 3D classification | Number classes: 5 / Software - Name: RELION (ver. 1.4) |
Final angle assignment | Type: PROJECTION MATCHING / Software - Name: RELION (ver. 1.4) |
Final reconstruction | Number classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 11.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 1.4) / Number images used: 5099 |