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- EMDB-3659: 601 nucleosome in complex with X. laevis histone H1.0b -

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Basic information

Entry
Database: EMDB / ID: 3659
Title601 nucleosome in complex with X. laevis histone H1.0b
Sample601 nucleosome in complex with X. laevis histone H1.0b
SourceXenopus laevis / amphibia / African clawed frog /
Map dataNucleosome in complex with X. laevis histone H1.0b
Methodsingle particle reconstruction, at 11.4 A 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
CitationMol. Cell, 2017, 66, 384-397.e8

Mol. Cell, 2017, 66, 384-397.e8 StrPapers
Structure and Dynamics of a 197 bp Nucleosome in Complex with Linker Histone H1.
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

DateDeposition: Apr 4, 2017 / Header (metadata) release: May 17, 2017 / Map release: May 17, 2017 / Last update: Apr 4, 2017

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.005
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by radius
  • Surface level: 0.005
  • Imaged by UCSF CHIMERA
  • Download
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Supplemental images

Downloads & links

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Map

Fileemd_3659.map.gz (map file in CCP4 format, 30119 KB)
Projections & slices

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

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 1.78 A
Density
Contour Level:0.005 (by author), 0.005 (movie #1):
Minimum - Maximum-0.034586214 - 0.06351287
Average (Standard dev.)1.9895606E-5 (0.0022681255)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions196196196
Origin-98-98-98
Limit979797
Spacing196196196
CellA=B=C: 348.88 A
Alpha=beta=gamma: 90 deg.

CCP4 map header:

modeImage stored as Reals
A/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
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS-98-98-98
NC/NR/NS196196196
D min/max/mean-0.0350.0640.000

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Supplemental data

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Sample components

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Entire 601 nucleosome in complex with X. laevis histone H1.0b

EntireName: 601 nucleosome in complex with X. laevis histone H1.0b
Number of components: 1

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Component #1: protein, 601 nucleosome in complex with X. laevis histone H1.0b

ProteinName: 601 nucleosome in complex with X. laevis histone H1.0b
Recombinant expression: No
SourceSpecies: Xenopus laevis / amphibia / African clawed frog /
Source (engineered)Expression System: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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Experimental details

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Sample preparation

Specimen stateparticle
Sample solutionSpecimen conc.: 0.3 mg/ml / pH: 7.2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 277 K / Humidity: 100 %

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Electron microscopy imaging

ImagingMicroscope: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 100 kV / Electron dose: 20 e/A2 / 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)

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 5099
3D reconstructionAlgorithm: FOURIER SPACE / Software: Relion / Resolution: 11.4 A / Resolution method: FSC 0.143 CUT-OFF

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