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Structural model of 53BP1 bound to a ubiquitylated and methylated nucleosome, at 4.5 A resolution
ELECTRON MICROSCOPY
Refinement
RMS Deviations
Key
Refinement Restraint Deviation
f_dihedral_angle_d
20.874
f_angle_d
0.963
f_chiral_restr
0.063
f_bond_d
0.009
f_plane_restr
0.006
Sample
NCP-ubme/GST-53BP1 complex
Sample Components
NCP-ubme
Widom-601 DNA
GST-53BP1
Ubiquitylated methylated histone octamer
Histone H4kc20Me2
Histone H3
Histone H2B.1
Histone H2A.1 K13RK36R
Ubiquitin
Specimen Preparation
Sample Aggregation State
PARTICLE
Vitrification Instrument
FEI VITROBOT MARK III
Cryogen Name
ETHANE-PROPANE
Sample Vitrification Details
Plunged into liquid ethane-propane (FEI VITROBOT MARK III)
3D Reconstruction
Reconstruction Method
SINGLE PARTICLE
Number of Particles
45361
Reported Resolution (Å)
4.54
Resolution Method
FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type
POINT
Point Symmetry
C2
Map-Model Fitting and Refinement
Id
1
Refinement Space
REAL
Refinement Protocol
RIGID BODY FIT
Refinement Target
Overall B Value
207.5
Fitting Procedure
Details
The atomic models of Widom-601 DNA (PDB ID 3LZ0), octameric histones (PDB ID 1KX5), ubiquitin (PDB ID 1UBI), and H4K20me2/53BP1 tandem Tudor domain (P ...
The atomic models of Widom-601 DNA (PDB ID 3LZ0), octameric histones (PDB ID 1KX5), ubiquitin (PDB ID 1UBI), and H4K20me2/53BP1 tandem Tudor domain (PDB ID 2IG0) were fitted without allowing flexibility into the 3D maps using UCSF Chimera. Segmentation was performed in UCSF Chimera. For the NCP-ubme structure the ubiquitin segmentation was further modified to remove obvious NCP density from the ubiquitin segment. The H2A/H2B sequence was mutated to the human H2AK13R/K36R and H2B manually in UCSF Chimera. A polyalanine model of the UDR was built within the UDR density in Coot, which compared well to predicted structures generated by Rosetta. The UDR model was mutated and fitted using UCSF Chimera, followed by iterative rounds of real-space refinement in PHENIX and model optimization in Coot. All figures were prepared in UCSF Chimera.
Data Acquisition
Detector Type
GATAN K2 SUMMIT (4k x 4k)
Electron Dose (electrons/Å**2)
36
Imaging Experiment
1
Date of Experiment
Temperature (Kelvin)
Microscope Model
FEI TECNAI F20
Minimum Defocus (nm)
Maximum Defocus (nm)
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS
2
Imaging Mode
BRIGHT FIELD
Specimen Holder Model
GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER
Nominal Magnification
25000
Calibrated Magnification
34483
Source
FIELD EMISSION GUN
Acceleration Voltage (kV)
200
Imaging Details
EM Software
Task
Software Package
Version
IMAGE ACQUISITION
DigitalMicrograph
2.31.691.0
CTF CORRECTION
CTFFIND
3
MODEL FITTING
UCSF Chimera
1.10.1
MODEL REFINEMENT
PHENIX
1.10.1.2115
INITIAL EULER ASSIGNMENT
RELION
1.3
FINAL EULER ASSIGNMENT
RELION
1.3
CLASSIFICATION
RELION
1.3
RECONSTRUCTION
RELION
1.3
Image Processing
CTF Correction Type
CTF Correction Details
Number of Particles Selected
Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION
174185
Automatically picked from roughly 3000 particles using a manually picked template