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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