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- PDB-8dft: Cryo-EM structure of conjugative pili from Pyrobaculum calidifontis -
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Open data
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Basic information
Entry | Database: PDB / ID: 8dft | ||||||
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Title | Cryo-EM structure of conjugative pili from Pyrobaculum calidifontis | ||||||
![]() | Pilin protein![]() | ||||||
![]() | PROTEIN FIBRIL / archaeal conjugative pilus | ||||||
Function / homology | ![]() ![]() | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Beltran, L.C. / Egelman, E.H. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Archaeal DNA-import apparatus is homologous to bacterial conjugation machinery. Authors: Leticia C Beltran / Virginija Cvirkaite-Krupovic / Jessalyn Miller / Fengbin Wang / Mark A B Kreutzberger / Jonasz B Patkowski / Tiago R D Costa / Stefan Schouten / Ilya Levental / Vincent P ...Authors: Leticia C Beltran / Virginija Cvirkaite-Krupovic / Jessalyn Miller / Fengbin Wang / Mark A B Kreutzberger / Jonasz B Patkowski / Tiago R D Costa / Stefan Schouten / Ilya Levental / Vincent P Conticello / Edward H Egelman / Mart Krupovic / ![]() ![]() ![]() ![]() Abstract: Conjugation is a major mechanism of horizontal gene transfer promoting the spread of antibiotic resistance among human pathogens. It involves establishing a junction between a donor and a recipient ...Conjugation is a major mechanism of horizontal gene transfer promoting the spread of antibiotic resistance among human pathogens. It involves establishing a junction between a donor and a recipient cell via an extracellular appendage known as the mating pilus. In bacteria, the conjugation machinery is encoded by plasmids or transposons and typically mediates the transfer of cognate mobile genetic elements. Much less is known about conjugation in archaea. Here, we determine atomic structures by cryo-electron microscopy of three conjugative pili, two from hyperthermophilic archaea (Aeropyrum pernix and Pyrobaculum calidifontis) and one encoded by the Ti plasmid of the bacterium Agrobacterium tumefaciens, and show that the archaeal pili are homologous to bacterial mating pili. However, the archaeal conjugation machinery, known as Ced, has been 'domesticated', that is, the genes for the conjugation machinery are encoded on the chromosome rather than on mobile genetic elements, and mediates the transfer of cellular DNA. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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PDBx/mmCIF format | ![]() | 396.9 KB | Display | ![]() |
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PDB format | ![]() | 340.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 27413MC ![]() 8dfuC ![]() 8exhC M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Components
#1: Protein | ![]() Mass: 11943.107 Da / Num. of mol.: 20 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() #2: Chemical | ChemComp-TT0 / [( Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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EM experiment | Aggregation state: FILAMENT / 3D reconstruction method: helical reconstruction |
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Sample preparation
Component | Name: P. calidifontis pilin protein / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: #1 / Source: NATURAL |
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Source (natural) | Organism: ![]() ![]() ![]() |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied![]() ![]() |
EM staining | Type: NEGATIVE / Material: uranyl acetate |
Specimen support | Grid type: EMS Lacey Carbon |
Vitrification![]() | Instrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 90 % / Details: blot for 3 seconds before plunging |
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Electron microscopy imaging
Microscopy | Model: FEI TITAN |
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Electron gun | Electron source![]() ![]() |
Electron lens | Mode: OTHER / Nominal defocus max: 2200 nm / Nominal defocus min: 1200 nm |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
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Processing
EM software | Name: cryoSPARC / Version: 3.2 / Category: 3D reconstruction![]() |
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CTF correction![]() | Type: PHASE FLIPPING ONLY |
Helical symmerty | Angular rotation/subunit: 74.206 ° / Axial rise/subunit: 5.001 Å / Axial symmetry: C1 |
3D reconstruction![]() | Resolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 71981 / Symmetry type: HELICAL |