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- EMDB-3675: Nucleosome core particle Ubiquitylated at H2A Lys-13 -

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Basic information

Entry
Database: EMDB / ID: 3675
TitleNucleosome core particle Ubiquitylated at H2A Lys-13
SampleNCP-ub complex
SourceDrosophila / arthropod / image: Drosophila melanogaster
Map dataNucleosome core particle with ubquitin covalently tethered to H2A lysine 13
Methodsingle particle reconstruction, at 8.8 A resolution
AuthorsWilson MD / Kitevski-LeBlanc J / Durocher D / Rubinstein JL / Kay LE
CitationElife, 2017, 6

Elife, 2017, 6 StrPapers
The RNF168 paralog RNF169 defines a new class of ubiquitylated histone reader involved in the response to DNA damage.
Julianne Kitevski-LeBlanc / Amélie Fradet-Turcotte / Predrag Kukic / Marcus D Wilson / Guillem Portella / Tairan Yuwen / Stephanie Panier / Shili Duan / Marella D Canny / Hugo van Ingen / Cheryl H Arrowsmith / John L Rubinstein / Michele Vendruscolo / Daniel Durocher / Lewis E Kay

DateDeposition: Apr 17, 2017 / Header (metadata) release: May 3, 2017 / Map release: May 3, 2017 / Last update: Apr 17, 2017

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.015
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by radius
  • Surface level: 0.015
  • Imaged by UCSF CHIMERA
  • Download
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Supplemental images

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Map

Fileemd_3675.map.gz (map file in CCP4 format, 8389 KB)
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
128 pix
1.45 A/pix
= 185.6 A
128 pix
1.45 A/pix
= 185.6 A
128 pix
1.45 A/pix
= 185.6 A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 1.45 A
Density
Contour Level:0.015 (by author), 0.015 (movie #1):
Minimum - Maximum-0.01582847 - 0.13095534
Average (Standard dev.)0.0036272337 (0.015028647)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions128128128
Origin000
Limit127127127
Spacing128128128
CellA=B=C: 185.6 A
Alpha=beta=gamma: 90 deg.

CCP4 map header:

modeImage stored as Reals
A/pix X/Y/Z1.451.451.45
M x/y/z128128128
origin x/y/z0.0000.0000.000
length x/y/z185.600185.600185.600
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS128128128
D min/max/mean-0.0160.1310.004

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Supplemental data

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Sample components

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Entire NCP-ub complex

EntireName: NCP-ub complex
Details: H2AK13 disulphide ubiquitylated Nucleosome core particle
Number of components: 2

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Component #1: protein, NCP-ub complex

ProteinName: NCP-ub complex
Details: H2AK13 disulphide ubiquitylated Nucleosome core particle
Recombinant expression: No

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Component #2: protein, H2AK13 ubiquitylated Nucleosome core particle

ProteinName: H2AK13 ubiquitylated Nucleosome core particle
Details: recombinant Drosophila histones wrapped with synthetic strong positioning Widom-601 DNA. Ubiquitin G76C covalently tethered to engineered K13C residue in H2A, prior to NCP reconstitution
Recombinant expression: No
SourceSpecies: Drosophila / arthropod / image: Drosophila melanogaster
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.: 0.65 mg/ml
Buffer solution: 10 mM Tris-Cl 17 pH 7.5, 50 mM KCl, 1 mM EDTA
pH: 7.5
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE-PROPANE MIXTURE / Temperature: 277 K / Humidity: 100 %

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Electron microscopy imaging

ImagingMicroscope: FEI TECNAI F20
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 36 e/A2 / Illumination mode: FLOOD BEAM
LensMagnification: 25000 X (nominal), 34483 X (calibrated) / Cs: 2 mm / Imaging mode: BRIGHT FIELD
Specimen HolderModel: GATAN LIQUID NITROGEN
CameraDetector: GATAN K2 (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 175

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C2 (2 fold cyclic) / Number of projections: 11063
3D reconstructionSoftware: RELION / Resolution: 8.8 A / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution assessment)

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