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Open data
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Basic information
Entry | ![]() | |||||||||
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Title | Agrobacterium tumefaciens Tpilus | |||||||||
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![]() | T-pilus / PROTEIN FIBRIL | |||||||||
Function / homology | Conjugal transfer TrbC/type IV secretion VirB2 / TrbC/VIRB2 pilin / type IV secretion system complex / protein secretion by the type IV secretion system / cell outer membrane / Protein virB2![]() | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | helical reconstruction / cryo EM / negative staining / Resolution: 3.5 Å | |||||||||
![]() | Beltran LC / Egelman EH | |||||||||
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
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 6.4 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 14.9 KB 14.9 KB | Display Display | ![]() |
Images | ![]() | 189.2 KB | ||
Filedesc metadata | ![]() | 5.3 KB | ||
Others | ![]() ![]() | 95.5 MB 95.5 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 976.8 KB | Display | ![]() |
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Full document | ![]() | 976.4 KB | Display | |
Data in XML | ![]() | 13.5 KB | Display | |
Data in CIF | ![]() | 15.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8exhMC ![]() 8dftC ![]() 8dfuC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Map
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Voxel size | X=Y=Z: 1.08 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #1
File | emd_28657_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_28657_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
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Sample components
-Entire : T-pilus Filament (VirB2 pilin subunit)
Entire | Name: T-pilus Filament (VirB2 pilin subunit) |
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Components |
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-Supramolecule #1: T-pilus Filament (VirB2 pilin subunit)
Supramolecule | Name: T-pilus Filament (VirB2 pilin subunit) / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1 / Details: Filaments generated by shearing off of bacteria |
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Source (natural) | Organism: ![]() |
-Macromolecule #1: Protein virB2
Macromolecule | Name: Protein virB2 / type: protein_or_peptide / ID: 1 / Number of copies: 40 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() Strain: C58 / ATCC 33970 |
Molecular weight | Theoretical: 6.803045 KDa |
Sequence | String: GGTDPATMVN NICTFILGPF GQSLAVLGIV AIGISWMFGR ASLGLVAGVV GGIVIMFGAS FLGKTLTGG UniProtKB: Protein virB2 |
-Macromolecule #2: (14S,17R)-20-amino-17-hydroxy-11,17-dioxo-12,16,18-trioxa-17lambd...
Macromolecule | Name: (14S,17R)-20-amino-17-hydroxy-11,17-dioxo-12,16,18-trioxa-17lambda~5~-phosphaicosan-14-yl tetradecanoate type: ligand / ID: 2 / Number of copies: 40 / Formula: X3D |
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Molecular weight | Theoretical: 593.773 Da |
Chemical component information | ![]() ChemComp-X3D: |
-Experimental details
-Structure determination
Method | negative staining, 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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Staining | Type: NEGATIVE / Material: Uranyl Acetate |
Grid | Model: EMS Lacey Carbon / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 298 K / Instrument: LEICA EM GP / Details: blot for 3 seconds before plunging. |
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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: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: OTHER / Imaging mode: OTHER / Cs: 2.7 mm / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.2 µm |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Final reconstruction | Applied symmetry - Helical parameters - Δz: 13.68 Å Applied symmetry - Helical parameters - Δ&Phi: 32.45 ° Applied symmetry - Helical parameters - Axial symmetry: C5 (5 fold cyclic) Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.1) / Number images used: 49308 |
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Startup model | Type of model: NONE |
Final angle assignment | Type: NOT APPLICABLE |