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- EMDB-3660: 601 nucleosome -

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Basic information

Database: EMDB / ID: 3660
Title601 nucleosome
Map data601 nucleosome
Sample601 nucleosome:
SourceXenopus laevis (African clawed frog)
Methodsingle particle reconstruction / cryo EM / 11.4 Å resolution
AuthorsBednar 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
CitationJournal: 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.
DateDeposition: Apr 4, 2017 / Header (metadata) release: May 17, 2017 / Map release: May 17, 2017 / Last update: Jul 12, 2017

Structure visualization

  • Surface view with section colored by density value
  • Surface level: 0.006
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.006
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
Supplemental images

Downloads & links


Fileemd_3660.map.gz (map file in CCP4 format, 30119 KB)
Projections & slices

Image control

AxesZ (Sec.)Y (Row.)X (Col.)
196 pix
1.78 Å/pix.
= 348.88 Å
196 pix
1.78 Å/pix.
= 348.88 Å
196 pix
1.78 Å/pix.
= 348.88 Å



Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.78 Å
Contour Level:0.006 (by author), 0.006 (movie #1):
Minimum - Maximum-0.029442614 - 0.071102045
Average (Standard dev.)6.95E-13 (0.0025464832)


Space Group Number1
Map Geometry
Axis orderXYZ
CellA=B=C: 348.88 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.781.781.78
M x/y/z196196196
origin x/y/z0.0000.0000.000
length x/y/z348.880348.880348.880
start NX/NY/NZ
MAP C/R/S123
start NC/NR/NS-102-102-102
D min/max/mean-0.0290.0710.000

Supplemental data

Sample components

Entire 601 nucleosome

EntireName: 601 nucleosome / Number of components: 1

Component #1: protein, 601 nucleosome

ProteinName: 601 nucleosome / Recombinant expression: No
SourceSpecies: Xenopus laevis (African clawed frog)
Source (engineered)Expression System: Escherichia coli (E. coli)

Experimental details

Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionSpecimen conc.: 0.3 mg/ml / pH: 7.2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 277 K / Humidity: 100 %

Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
ImagingMicroscope: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 100 kV / Electron dose: 20 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 59000 X (nominal), 78652 X (calibrated) / Cs: 2 mm / Imaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: FEI FALCON I (4k x 4k)

Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 29222
3D reconstructionAlgorithm: FOURIER SPACE / Software: RELION / Resolution: 11.4 Å / Resolution method: FSC 0.143 CUT-OFF

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