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- EMDB-22460: Cryo-EM structure of conjugative pili from carbapenem-resistant K... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-22460 | |||||||||
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Title | Cryo-EM structure of conjugative pili from carbapenem-resistant Klebsiella pneumoniae | |||||||||
![]() | Cryo-EM structure of conjugative pili from carbapenem-resistant Klebsiella pneumoniae | |||||||||
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![]() | Conjugation pili / Helical reconstruction / PROTEIN FIBRIL | |||||||||
Function / homology | TraA / TraA / : / membrane => GO:0016020 / extracellular region / plasma membrane / Pilin / Pilin![]() | |||||||||
Biological species | ![]() | |||||||||
Method | helical reconstruction / cryo EM / Resolution: 3.9 Å | |||||||||
![]() | Zheng W / Pena A | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Cryoelectron-Microscopic Structure of the pKpQIL Conjugative Pili from Carbapenem-Resistant Klebsiella pneumoniae. Authors: Weili Zheng / Alejandro Pena / Wen Wen Low / Joshua L C Wong / Gad Frankel / Edward H Egelman / ![]() ![]() Abstract: Conjugative pili are important in mediating bacterial conjugation and horizontal gene transfer. Since plasmid transfer can include antibiotic-resistance genes, conjugation is an important mechanism ...Conjugative pili are important in mediating bacterial conjugation and horizontal gene transfer. Since plasmid transfer can include antibiotic-resistance genes, conjugation is an important mechanism in the spread of antibiotic resistance. Filamentous bacteriophages have been shown to exist in two different structural classes: those with a 5-fold rotational symmetry and those with a one-start helix with approximately 5 subunits per turn. Structures for the F and the F-like pED208 conjugation pilus have shown that they have 5-fold rotational symmetry. Here, we report the cryoelectron-microscopic structure of conjugative pili from carbapenem-resistant Klebsiella pneumoniae, encoded on the IncFIIK pKpQIL plasmid, at 3.9 Å resolution and show that it has a one-start helix. These results establish that conjugation pili can exist in at least two structural classes, consistent with other results showing that relatively small perturbations are needed to change the helical symmetry of polymers. | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 59.5 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 9.8 KB 9.8 KB | Display Display | ![]() |
Images | ![]() | 183.1 KB | ||
Filedesc metadata | ![]() | 4.8 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7jsvMC M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Cryo-EM structure of conjugative pili from carbapenem-resistant Klebsiella pneumoniae | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.08 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : pKpQIL pili
Entire | Name: pKpQIL pili |
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Components |
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-Supramolecule #1: pKpQIL pili
Supramolecule | Name: pKpQIL pili / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: ![]() |
-Macromolecule #1: Pilin
Macromolecule | Name: Pilin / type: protein_or_peptide / ID: 1 / Number of copies: 41 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 7.324663 KDa |
Sequence | String: TTTATDLMKS GDATVKGTFG KQSSVVKWVV LAEVVAGGIM YMMTKNVKFL FGFAIISTFI TIGMSVAGY UniProtKB: Pilin |
-Macromolecule #2: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
Macromolecule | Name: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / type: ligand / ID: 2 / Number of copies: 41 / Formula: LHG |
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Molecular weight | Theoretical: 722.97 Da |
Chemical component information | ![]() ChemComp-LHG: |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | helical reconstruction |
Aggregation state | filament |
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Sample preparation
Buffer | pH: 7.5 |
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Grid | Pretreatment - Type: PLASMA CLEANING / Details: unspecified |
Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 55.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Sample stage | Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Final reconstruction | Applied symmetry - Helical parameters - Δz: 2.7 Å Applied symmetry - Helical parameters - Δ&Phi: 77.6 ° Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric) Resolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 163128 |
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Segment selection | Number selected: 263265 |
Startup model | Type of model: OTHER |
Final angle assignment | Type: NOT APPLICABLE |