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- EMDB-3657: Nucleosome in complex with human histone H1.5dC50 -

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Basic information

Entry
Database: EMDB / ID: 3657
TitleNucleosome in complex with human histone H1.5dC50
Samplenucleosome in complex with human H1.5dC50
SourceHomo sapiens / human
Map dataHuman H1.5%u0394C50-bound nucleosome
Methodsingle particle reconstruction, at 6.2 Å resolution
AuthorsBednar J / Garcia-Saez I / Boopathi R / Cutter AR / Papai G / Reymer A / Syed SH / Lone IN / Tonchev O / Crucifix 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 Yorodumi Papers
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: Mar 31, 2017 / Header (metadata) release: May 17, 2017 / Map release: May 17, 2017 / Last update: Aug 2, 2017

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.05
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by radius
  • Surface level: 0.05
  • Imaged by UCSF CHIMERA
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Supplemental images

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Map

Fileemd_3657.map.gz (map file in CCP4 format, 8389 KB)
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
128 pix
2.7 Å/pix.
= 345.6 Å
128 pix
2.7 Å/pix.
= 345.6 Å
128 pix
2.7 Å/pix.
= 345.6 Å

Surface

Projections

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Slices (1/2)

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Images are generated by Spider package.

Voxel sizeX=Y=Z: 2.7 Å
Density
Contour Level:0.03 (by author), 0.05 (movie #1):
Minimum - Maximum-0.2799674 - 0.45620975
Average (Standard dev.)0.00023675688 (0.015440903)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions128128128
Origin000
Limit127127127
Spacing128128128
CellA=B=C: 345.6 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.72.72.7
M x/y/z128128128
origin x/y/z0.0000.0000.000
length x/y/z345.600345.600345.600
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS128128128
D min/max/mean-0.2800.4560.000

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Supplemental data

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Sample components

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Entire nucleosome in complex with human H1.5dC50

EntireName: nucleosome in complex with human H1.5dC50 / Number of components: 1

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Component #1: protein, nucleosome in complex with human H1.5dC50

ProteinName: nucleosome in complex with human H1.5dC50 / Recombinant expression: No
SourceSpecies: Homo sapiens / human
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.: 0.5 mg/ml / pH: 7.1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 277.15 K / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 7.14 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 47000 X (nominal), 103703 X (calibrated) / Cs: 0.01 mm / Imaging mode: BRIGHT FIELD
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: FEI FALCON II (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 30619
3D reconstructionAlgorithm: FOURIER SPACE / Software: RELION / Resolution: 6.2 Å / Resolution method: FSC 0.143 CUT-OFF

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