7PEL | pdb_00007pel

CryoEM structure of simian T-cell lymphotropic virus intasome in complex with PP2A regulatory subunit B56 gamma

ELECTRON MICROSCOPY

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6QBW
experimental model	PDB	6TOQ
experimental model	PDB	6TJU
experimental model	PDB	5JJA

Refinement

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	23.148
f_angle_d	0.56
f_chiral_restr	0.041
f_bond_d	0.004
f_plane_restr	0.004

Sample
Complex of STLV-1 MarB43 integrase with nascent viral DNA and the human PP2A B56 subunit
Sample Components
Pol protein
Isoform 3 of PC4 and SFRS1-interacting protein,Isoform Gamma-2 of Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit gamma isoform
DNA

Specimen Preparation
Sample Aggregation State	PARTICLE
Vitrification Instrument	FEI VITROBOT MARK IV
Cryogen Name	ETHANE
Sample Vitrification Details

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	161921
Reported Resolution (Å)	3.34
Resolution Method	FSC 0.143 CUT-OFF
Other Details	3D reconstruction, including Bayesian particle polishing, CTF and beam tilt refinement, as implemented in Relion-3.1, resulted in the final map with minimal anisotropy; 3D-FSC sphericity index of the final map was 0.967.
Refinement Type
Symmetry Type	POINT
Point Symmetry	C2

Map-Model Fitting and Refinement
Id	1 (6QBW, 6TOQ, 6TJU, 5JJA)
Refinement Space	REAL
Refinement Protocol	RIGID BODY FIT
Refinement Target
Overall B Value	31.31
Fitting Procedure
Details

Data Acquisition
Detector Type	FEI FALCON III (4k x 4k)
Electron Dose (electrons/Å**2)	50.4

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	FEI TITAN KRIOS
Minimum Defocus (nm)
Maximum Defocus (nm)
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS
Imaging Mode	BRIGHT FIELD
Specimen Holder Model
Nominal Magnification
Calibrated Magnification
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	300
Imaging Details

EM Software
Task	Software Package	Version
PARTICLE SELECTION	Gautomatch
CTF CORRECTION	Gctf	1.06
MODEL FITTING	UCSF Chimera	1.12
MODEL FITTING	NAMD	Namdinator
MODEL FITTING	Coot	0.8.9.2
MODEL REFINEMENT	PHENIX	1.18-3845
MODEL REFINEMENT	Coot	0.8.9.2
INITIAL EULER ASSIGNMENT	cryoSPARC	2
CLASSIFICATION	RELION	3.1
RECONSTRUCTION	RELION	3.1

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION		4356108	2,198,454 (OH dataset) and 2,157,654 (GO dataset) 3D reconstructions using either separate subsets resulted in highly anisotropic maps due to severe preferential orientations. Because 3D-FCS analysis indicated favourable complementarity of the data, the datasets were merged as separate optic groups in Relion-3.1. 3D reconstruction, including Bayesian particle polishing, CTF and beam tilt refinement, as implemented in Relion-3.1, resulted in the final map with minimal anisotropy; 3D-FSC sphericity index of the final map was 0.967.