+
Open data
-
Basic information
Entry | Database: EMDB / ID: EMD-3996 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | N4 ring of PilQ from Thermus thermophilus | |||||||||
![]() | None | |||||||||
![]() |
| |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 6.5 Å | |||||||||
![]() | D'Imprima E / Vonck J / Sanchez R | |||||||||
![]() | ![]() Title: Cryo-EM structure of the bifunctional secretin complex of . Authors: Edoardo D'Imprima / Ralf Salzer / Ramachandra M Bhaskara / Ricardo Sánchez / Ilona Rose / Lennart Kirchner / Gerhard Hummer / Werner Kühlbrandt / Janet Vonck / Beate Averhoff / ![]() Abstract: Secretins form multimeric channels across the outer membrane of Gram-negative bacteria that mediate the import or export of substrates and/or extrusion of type IV pili. The secretin complex of is an ...Secretins form multimeric channels across the outer membrane of Gram-negative bacteria that mediate the import or export of substrates and/or extrusion of type IV pili. The secretin complex of is an oligomer of the 757-residue PilQ protein, essential for DNA uptake and pilus extrusion. Here, we present the cryo-EM structure of this bifunctional complex at a resolution of ~7 Å using a new reconstruction protocol. Thirteen protomers form a large periplasmic domain of six stacked rings and a secretin domain in the outer membrane. A homology model of the PilQ protein was fitted into the cryo-EM map. A crown-like structure outside the outer membrane capping the secretin was found not to be part of PilQ. Mutations in the secretin domain disrupted the crown and abolished DNA uptake, suggesting a central role of the crown in natural transformation. | |||||||||
History |
|
-
Structure visualization
Movie |
![]() |
---|---|
Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
-
Downloads & links
-EMDB archive
Map data | ![]() | 510.9 KB | ![]() | |
---|---|---|---|---|
Header (meta data) | ![]() ![]() | 10.9 KB 10.9 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 4.3 KB | Display | ![]() |
Images | ![]() | 14.4 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 217.2 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 216.4 KB | Display | |
Data in XML | ![]() | 9.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
-
Links
EMDB pages | ![]() ![]() |
---|
-
Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | None | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.63 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-
Sample components
-Entire : PilQ complex with 13-fold symmetry
Entire | Name: PilQ complex with 13-fold symmetry |
---|---|
Components |
|
-Supramolecule #1: PilQ complex with 13-fold symmetry
Supramolecule | Name: PilQ complex with 13-fold symmetry / type: complex / ID: 1 / Parent: 0 |
---|---|
Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 1 MDa |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
![]() | single particle reconstruction |
Aggregation state | particle |
-
Sample preparation
Buffer | pH: 8.5 |
---|---|
Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 70 % / Chamber temperature: 283 K / Instrument: FEI VITROBOT MARK IV / Details: blotting for 8-10 seconds. |
-
Electron microscopy
Microscope | JEOL 3200FSC |
---|---|
Specialist optics | Energy filter - Name: In-column Omega Filter / Energy filter - Lower energy threshold: 18 eV / Energy filter - Upper energy threshold: 18 eV |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Frames/image: 2-45 / Average exposure time: 9.0 sec. / Average electron dose: 33.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Calibrated magnification: 30675 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 4.2 mm / Nominal magnification: 20000 |
Sample stage | Specimen holder model: JEOL / Cooling holder cryogen: NITROGEN |