2024-09-18 REL PDBe PDBe PDBe 2024-02-27 2024-07-24 2024-07-24 2024-09-18 Wellcome Trust 217089 United Kingdom Cryo-EM Structure of the R388 plasmid conjugative pilus reveals a helical polymer characterised by an unusual pilin/phospholipid binary complex Vadakkepat AK Waksman G Redzej A Conjugal transfer protein, VirB2, Conjugative pilus, Type-4 secretion system fibre, Conduit for horizontal gene transfer, anti-microbial resistance, PROTEIN FIBRIL Vadakkepat AK Xue S Redzej A Smith TK Ho BT Waksman G Cryo-EM structure of the R388 plasmid conjugative pilus reveals a helical polymer characterized by an unusual pilin/phospholipid binary complex. Structure UK 32 1335 2024 39002540 doi:10.1016/j.str.2024.06.009 0969-2126 2005 STRUE6 8s6h FULLOVERLAP Conjugative pilus from the E. coli R388 plasmid Conjugative pilus from the E. coli R388 plasmid 0 1
Helical filament called the conjugative pilus. This is part of the type-4 secretion system. Monomeric unit of the complex comprises of the protein VirB2/TrwL (for R388 pilus) and a lipid PG 32.1
Escherichia coli HB101 Cell Surface 7.39 TrwL protein Escherichia coli HB101 0.007396732
The first 43 amino acids have been cleaved off from the pro-pilin TrwL/VirB2 during post-translational processing for maturation.
69 LEVO AQGLEKARSVLETLQQELTTIVPIAAAVILLCLGIAYAGRFIEKDTFVRWSIGVIIAGSAVQITAMLFT O50328 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE 0.00072297 69 LHG helical helicalArray 0.25 7.4 10.0 Na2HPO4 Sodium Phosphate 1.8 KH2PO4 Potassium Phosphate 2.7 KCl Potassium Chloride 2.7 NaCl Sodium Chloride
Phosphate buffer saline
 C-flat-1.2/1.3 COPPER/PALLADIUM 400 GRAPHENE OXIDE CONTINUOUS 100.0 GLOW DISCHARGE ETHANE 100 277.15 FEI VITROBOT MARK IV
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..
This specimen was purified to high levels.
 FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 2.7 0.9 0.9 2.4 2.4 81000.0 81000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN 80.0 80.0
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.
GATAN K3 BIOQUANTUM (6k x 4k) 4884 34.67
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. Data were collected using the EPU software with a defocus range 0.9 micrometer to 2.4 micrometer and a total of 4884 movies were collected.
 1
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3 13.241 28.983 C1 3.39 FSC 0.143 CUT-OFF cryoSPARC CRYOSPARC v4.3.1
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209930 1158759 cryoSPARC CRYOSPARC v4.3.1
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 NOT APPLICABLE cryoSPARC CRYOSPARC v4.3.1
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 emd_19758.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 400 400 400 0 0 0 400 400 400 426.80002 426.80002 426.80002 90.0 90.0 90.0 X Y Z -1.0331122 2.2909944 0.0002951389 0.08620985 1.067 1.067 1.067 0.321 AUTHOR Sharpened map of the R388 Pilus filament generated using cryosparc AlphaFold in silico model RIGID BODY FIT
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Cross-correlation in Phenix 109.700000000000003 emd_19758_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 400 400 400 0 0 0 400 400 400 426.80002 426.80002 426.80002 90.0 90.0 90.0 X Y Z -0.52427363 1.107906 0.0006985617 0.07670593 1.067 1.067 1.067 AUTHOR Halfmap-A of the R388 Pilus filament generated using cryosparc and used to calculate the FSC curve using LocalResolution in Cryosparc. The resulting FSC curve shown in the associated publication. emd_19758_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 400 400 400 0 0 0 400 400 400 426.80002 426.80002 426.80002 90.0 90.0 90.0 X Y Z -0.5679981 1.1584297 0.0007798614 0.07678754 1.067 1.067 1.067 AUTHOR Halfmap-B of the R388 Pilus filament generated using cryosparc and used to calculate the FSC curve using LocalResolution in Cryosparc. The resulting FSC curve shown in the associated publication.