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Nucleosome core particle Ubiquitylated at H2A Lys-13

by single particle reconstruction, at 8.8 A resolution

Movie

Orientation:

#1: Surface view with section colored by density value, Surface level: 0.015, Imaged by UCSF CHIMERA

#2: Surface view colored by radius, Surface level: 0.015, Imaged by UCSF CHIMERA

Entry
Summary
Database / IDEM DATA BANK (EMDB) / 3675
TitleNucleosome core particle Ubiquitylated at H2A Lys-13
MapNucleosome core particle with ubquitin covalently tethered to H2A lysine 13
SampleNCP-ub complex
AuthorsWilson MD, Kitevski-LeBlanc J, Durocher D, Rubinstein JL, Kay LE
DateDeposition: 2017-04-17, Header release: 2017-05-03, Map release: 2017-05-03, Last update: 2017-07-12
EMDB SitesEMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
MoviesMovie Page

#1: Surface view with section colored by density value, Surface level: 0.015, Imaged by UCSF CHIMERA

#2: Surface view colored by radius, Surface level: 0.015, Imaged by UCSF CHIMERA

Supplemental images
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Related Structure Data
Related Entries

Cite: data citing same article

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Article
Citation - Primary
ArticleElife, Vol. 6, Year 2017
TitleThe RNF168 paralog RNF169 defines a new class of ubiquitylated histone reader involved in the response to DNA damage.
AuthorsJulianne 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
Department of Molecular Genetics, University of Toronto, Toronto, Canada.
Department of Biochemistry, University of Toronto, Toronto, Canada.
Department of Chemistry, University of Toronto, Toronto, Canada.
The Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Canada.
Laval University Cancer Research Center, Oncology Axis - Centre Hospitalier Universitaire de Québec Research Center - Université Laval, Hôtel-Dieu de Québec, Québec City, Canada.
Department of Chemistry, University of Cambridge, Cambridge, United Kingdom.
Structural Genomics Consortium, University of Toronto, Toronto, Canada.
Princess Margret Cancer Centre, Toronto, Canada.
Department of Medical Biophysics, University of Toronto, Toronto, Canada.
Macromolecular Biochemistry, Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands.
Molecular Structure and Function Program, The Hospital for Sick Children Research Institute, Toronto, Canada.
LinksPubMed: 28406400, DOI: 10.7554/eLife.23872, PMC: PMC5426901
Map
Fileemd_3675.map.gz ( map file in CCP4 format, 8389 KB )
Projections & SlicesSize of images:
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.

Density
Contour Level:0.015 (by author), 0.015 (movie #1):
Minimum - Maximum: -0.01582847 - 0.13095534
Average (Standard dev.): 0.0036272337 (0.015028647)
Data TypeImage stored as Reals
Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions128128128
Origin000
Limit127127127
Spacing128128128
Unit CellA= B= C: 185.6 A
Alpha=beta=gamma: 90 degrees
Pixel SpacingX= Y= Z: 1.45 A
CCP4 map header info
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
start NC,NX/NR,NY/NS,NZ
NC,NX/NR,NY/NS,NZ
D min/max/mean-0.0160.1310.004
Annotation DetailsNucleosome core particle with ubquitin covalently tethered to H2A lysine 13
Supplement
Images
Images
FSC
FSC
Sample
NameNCP-ub complex
Number of Components2
DetailsH2AK13 disulphide ubiquitylated Nucleosome core particle
Component #1: protein - NCP-ub complex
Scientific nameNCP-ub complex
DetailsH2AK13 disulphide ubiquitylated Nucleosome core particle
Recombinant expressionNo
Component #2: protein - H2AK13 ubiquitylated Nucleosome core particle
Scientific nameH2AK13 ubiquitylated Nucleosome core particle
Detailsrecombinant Drosophila histones wrapped with synthetic strong positioning Widom-601 DNA. Ubiquitin G76C covalently tethered to engineered K13C residue in H2A, prior to NCP reconstitution
Scientific Name of SpeciesDrosophila
NCBI taxonomy7215
Recombinant expressionNo
Engineered SourceNCBI taxonomy: 562
Expression system: Escherichia coli
Experiment
Sample Preparation
Specimen Stateparticle
Specimen Conc0.65 mg/ml
BufferpH: 7.5
Details: 10 mM Tris-Cl 17 pH 7.5, 50 mM KCl, 1 mM EDTA
Vitrification
Cryogen NameETHANE-PROPANE MIXTURE
Humidity100
Temperature277 Kelvin
InstrumentFEI VITROBOT MARK III
Imaging
MicroscopeFEI TECNAI F20
Electron Gun
Electron SourceFIELD EMISSION GUN
Accelerating Voltage200 kV
Electron Dose36 e/A**2
Illumination ModeFLOOD BEAM
Lens
MagnificationNominal: 25000, Calibrated: 34483
Nominal Cs2 mm
Imaging ModeBRIGHT FIELD
Specimen Holder
ModelGATAN LIQUID NITROGEN
Camera
DetectorGATAN K2 (4k x 4k)
Image Acquisition
#1
Number of Digital Images175
Processing
Methodsingle particle reconstruction
3D reconstruction
SoftwareRELION
Resolution By Author
8.8 A
Resolution MethodFSC 0.143 CUT-OFF
Single Particle
Applied SymmetryC2 (2 fold cyclic)
Number of Projections11063
Download
Data from EMDB
Header (meta data in XML format)emd-3675-v19.xml (6.6 KB)
emd-3675-v20.xml (11.8 KB)
emd-3675.xml (6.6 KB)
Map dataemd_3675.map.gz (3.9 MB)
Imagesemd_3675.png (38 KB)
FSC (resolution estimation)emd_3675_fsc.xml (4.5 KB)
FTP directoryftp://ftp.pdbj.org/pub/emdb/structures/EMD-3675
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 3.5 MB
.webm (WebM/VP8 format), 4.8 MB
Session file for UCSF-Chimera, 26.9 KB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3.2 MB
.webm (WebM/VP8 format), 5 MB
Session file for UCSF-Chimera, 26.9 KB