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- EMDB-4046: Cryo-EM structure of the bacterial sex F pilus (12.5 Angstrom rise) -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-4046 | ||||||||||||
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Title | Cryo-EM structure of the bacterial sex F pilus (12.5 Angstrom rise) | ||||||||||||
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![]() | F-pilus Conjugation Type IV secretion system Phospholipid / Protein fibril | ||||||||||||
Function / homology | TraA / TraA / extracellular region / plasma membrane / Pilin / Pilin![]() | ||||||||||||
Biological species | ![]() ![]() | ||||||||||||
Method | helical reconstruction / cryo EM / Resolution: 5.0 Å | ||||||||||||
![]() | Costa TRD / Ilangovan I | ||||||||||||
Funding support | ![]() ![]()
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![]() | ![]() Title: Structure of the Bacterial Sex F Pilus Reveals an Assembly of a Stoichiometric Protein-Phospholipid Complex. Authors: Tiago R D Costa / Aravindan Ilangovan / Marta Ukleja / Adam Redzej / Joanne M Santini / Terry K Smith / Edward H Egelman / Gabriel Waksman / ![]() ![]() Abstract: Conjugative pili are widespread bacterial appendages that play important roles in horizontal gene transfer, in spread of antibiotic resistance genes, and as sites of phage attachment. Among ...Conjugative pili are widespread bacterial appendages that play important roles in horizontal gene transfer, in spread of antibiotic resistance genes, and as sites of phage attachment. Among conjugative pili, the F "sex" pilus encoded by the F plasmid is the best functionally characterized, and it is also historically the most important, as the discovery of F-plasmid-mediated conjugation ushered in the era of molecular biology and genetics. Yet, its structure is unknown. Here, we present atomic models of two F family pili, the F and pED208 pili, generated from cryoelectron microscopy reconstructions at 5.0 and 3.6 Å resolution, respectively. These structures reveal that conjugative pili are assemblies of stoichiometric protein-phospholipid units. We further demonstrate that each pilus type binds preferentially to particular phospholipids. These structures provide the molecular basis for F pilus assembly and also shed light on the remarkable properties of conjugative pili in bacterial secretion and phage infection. | ||||||||||||
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 | ![]() | 2.1 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 10.6 KB 10.6 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 4.6 KB | Display | ![]() |
Images | ![]() | 305 KB | ||
Filedesc metadata | ![]() | 4.8 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 257.9 KB | Display | ![]() |
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Full document | ![]() | 257 KB | Display | |
Data in XML | ![]() | 7.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5lfbMC ![]() 4042C ![]() 4044C ![]() 5legC ![]() 5lerC 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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Projections & slices | Image control
Images are generated by Spider. generated in cubic-lattice coordinate | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.1 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 : F-pilus filament made by an assembly of a stoichiometric protein-...
Entire | Name: F-pilus filament made by an assembly of a stoichiometric protein-phospholipid complex |
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Components |
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-Supramolecule #1: F-pilus filament made by an assembly of a stoichiometric protein-...
Supramolecule | Name: F-pilus filament made by an assembly of a stoichiometric protein-phospholipid complex type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 7.3 kDa/nm |
-Macromolecule #1: Pilin
Macromolecule | Name: Pilin / type: protein_or_peptide / ID: 1 / Number of copies: 75 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 6.831216 KDa |
Sequence | String: QDLMASGNTT VKATFGKDSS VVKWVVLAEV LVGAVMYMMT KNVKFLAGFA IISVFIAVGM AVVGL UniProtKB: Pilin |
-Macromolecule #2: [(2~{S})-3-[[(2~{R})-2,3-bis(oxidanyl)propoxy]-oxidanyl-phosphory...
Macromolecule | Name: [(2~{S})-3-[[(2~{R})-2,3-bis(oxidanyl)propoxy]-oxidanyl-phosphoryl]oxy-2-hexadec-9-enoyloxy-propyl] hexadecanoate type: ligand / ID: 2 / Number of copies: 75 / Formula: 6V6 |
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Molecular weight | Theoretical: 720.954 Da |
Chemical component information | ![]() ChemComp-6V6: |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | helical reconstruction |
Aggregation state | helical array |
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Sample preparation
Buffer | pH: 8 |
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Grid | Model: Lacey / Material: COPPER / Mesh: 400 |
Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI POLARA 300 |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 1.67 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | ![]() Model: Tecnai Polara / Image courtesy: FEI Company |
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Image processing
-Atomic model buiding 1
Refinement | Protocol: AB INITIO MODEL |
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Output model | ![]() PDB-5lfb: |