8S6H | pdb_00008s6h

Cryo-EM Structure of the R388 plasmid conjugative pilus reveals a helical polymer characterised by an unusual pilin/phospholipid binary complex

ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold

Refinement

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	10.2606
f_angle_d	0.3786
f_chiral_restr	0.0349
f_bond_d	0.0033
f_plane_restr	0.0024

Sample
Conjugative pilus from the E. coli R388 plasmid

Specimen Preparation
Sample Aggregation State	HELICAL ARRAY
Vitrification Instrument	FEI VITROBOT MARK IV
Cryogen Name	ETHANE
Sample Vitrification Details	C-flat grids (Protochips, US 1.2/1.3 400 mesh) were negatively glow discharged using PELCO Easiglow (Ted Pella, USA) and coated with graphene oxide. 3 ...	C-flat grids (Protochips, US 1.2/1.3 400 mesh) were negatively glow discharged using PELCO Easiglow (Ted Pella, USA) and coated with graphene oxide. 3 microliter of the purified pili sample was applied on each grid and a Vitrobot Mark IV (Thermo Fisher Scientific, USA) operating at 4C and 100 percent humidity was used to incubate the sample on the grid for 30 secs and blotting for 16 secs (blot force -10) prior to vitrification in liquid ethane.

3D Reconstruction
Reconstruction Method	HELICAL
Number of Particles	209930
Reported Resolution (Å)	3.39
Resolution Method	FSC 0.143 CUT-OFF
Other Details	Find more details in the Methods section of the publication
Refinement Type
Symmetry Type	HELICAL
Axial Symmetry	C1
Axial Rise	13.241
Angular Rotation	28.983

Map-Model Fitting and Refinement
Id	1
Refinement Space
Refinement Protocol	RIGID BODY FIT
Refinement Target	Cross-correlation in Phenix
Overall B Value	109.7
Fitting Procedure
Details	Find more details in the Methods section of the publication

Data Acquisition
Detector Type	GATAN K3 BIOQUANTUM (6k x 4k)
Electron Dose (electrons/Å**2)	34.67

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	FEI TITAN KRIOS
Minimum Defocus (nm)	900
Maximum Defocus (nm)	2400
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS	2.7
Imaging Mode	BRIGHT FIELD
Specimen Holder Model	FEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification	81000
Calibrated Magnification	81000
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	300
Imaging Details	The R388 pilus data were collected at the ISMB Birkbeck EM facility using a Titan Krios microscope (Thermo Fisher Scientific, USA) operated at 300 keV and equipped with a BioQuantum energy filter (Gatan, USA) with a slit width of 20 eV. The images were collected with a post-GIF K3 direct electron detector (Gatan, USA) operating in super resolution mode, at a magnification of 81,000 corresponding to a pixel size of 1.067 A. The dose rate was set to 14.62 e per pixel per second and a total dose of 34.67 e per A2 was fractionated over 50 frames.

EM Software
Task	Software Package	Version
PARTICLE SELECTION	cryoSPARC	CRYOSPARC v4.3.1
IMAGE ACQUISITION	EPU
CTF CORRECTION	cryoSPARC	CRYOSPARC v4.3.1
MODEL FITTING	Coot	COOT v0.9.3
INITIAL EULER ASSIGNMENT	cryoSPARC	CRYOSPARC v4.3.1
FINAL EULER ASSIGNMENT	cryoSPARC	CRYOSPARC v4.3.1
CLASSIFICATION	cryoSPARC	CRYOSPARC v4.3.1
RECONSTRUCTION	cryoSPARC	CRYOSPARC v4.3.1
MODEL REFINEMENT	PHENIX	1.21rc1_5058

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION	Find more details in the Methods section of the publication	1158759	Find more details in the Methods section of the publication

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.