6GYB

Cryo-EM structure of the bacteria-killing type IV secretion system core complex from Xanthomonas citri

ELECTRON MICROSCOPY

Refinement

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	10.324
f_angle_d	0.892
f_chiral_restr	0.06
f_bond_d	0.008
f_plane_restr	0.007

Sample
Core complex of a bacterial killing type IV secretion system from Xanthomonas

Specimen Preparation
Sample Aggregation State	PARTICLE
Vitrification Instrument	FEI VITROBOT MARK IV
Cryogen Name	ETHANE
Sample Vitrification Details	Blot for 4.5 seconds after 30 seconds of incubation.

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	142306
Reported Resolution (Å)	3.28
Resolution Method	FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type	POINT
Point Symmetry	C14

Map-Model Fitting and Refinement
Id	1
Refinement Space	REAL
Refinement Protocol
Refinement Target	Cross-correlation coefficient
Overall B Value	138
Fitting Procedure
Details	The electron density was clearly interpretable, which allowed us to build a de novo structural model. This process began by fitting the crystallograph ...	The electron density was clearly interpretable, which allowed us to build a de novo structural model. This process began by fitting the crystallographic model of the X. citri VirB7 C-terminal N0 domain (PDB:3OV5) and the NMR model of the X. citri VirB9CTD-VirB7NTD complex (PDB:2N01) in order to identify the map with the correct handedness. Models were positioned using Fit in map tool in Chimera, and saved relative to the map. Using these as starting points, we were able to manually build the rest of the model for VirB7 and VirB9CTD, and the de novo models for VirB10CTD, VirB10NTD_150-161 and VirB9NTD using Coot. In this manner, we obtained a combined model for a single VirB7-VirB9-VirB10 heterotrimer unit, which was submitted to iterative rounds of real space refinement and building using PHENIX and Coot software, respectively. Thirteen more copies of the refined heterotrimer were then fit into the density map using Chimera and new rounds of real space refinement (now using NCS for the 42 chains contained in the structure) and building using PHENIX and Coot, respectively, were executed until we obtained good parameters for Ramachandran plot and MolProbity. Chimera and PyMol were used for map and model visualization and figure production.

Data Acquisition
Detector Type	GATAN K2 QUANTUM (4k x 4k)
Electron Dose (electrons/Å**2)	60

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	RELION	2.0
IMAGE ACQUISITION	EPU	1.8
CTF CORRECTION	Gctf	1.06
MODEL FITTING	Coot	0.8.6
MODEL FITTING	UCSF Chimera	8.6.1
INITIAL EULER ASSIGNMENT	cryoSPARC	1.0
FINAL EULER ASSIGNMENT	RELION	2.0
CLASSIFICATION	RELION	2.0
RECONSTRUCTION	RELION	2.0
MODEL REFINEMENT	PHENIX	1.12

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION		185079

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.