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- PDB-5oiu: Crystal structure of PilF type IV pilus assembly ATPase from Ther... -
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Basic information
Entry | Database: PDB / ID: 5oiu | ||||||
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Title | Crystal structure of PilF type IV pilus assembly ATPase from Thermus thermophilus | ||||||
![]() | Type IV pilus assembly protein PilF | ||||||
![]() | MOTOR PROTEIN / ATPase / AAA+ / type IV pilus / DNA binding protein / ATP | ||||||
Function / homology | ![]() ATP hydrolysis activity / ATP binding / metal ion binding / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Karuppiah, V. / Derrick, J.P. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structural cycle of the Thermus thermophilus PilF ATPase: the powering of type IVa pilus assembly. Authors: Richard Collins / Vijaykumar Karuppiah / C Alistair Siebert / Rana Dajani / Angela Thistlethwaite / Jeremy P Derrick / ![]() Abstract: Type IV pili are responsible for a diverse range of functions, including twitching motility and cell adhesion. Assembly of the pilus fiber is driven by a cytoplasmic ATPase: it interacts with an ...Type IV pili are responsible for a diverse range of functions, including twitching motility and cell adhesion. Assembly of the pilus fiber is driven by a cytoplasmic ATPase: it interacts with an inner membrane complex of biogenesis proteins which, in turn, bind to nascent pilin subunits and mediate fiber assembly. Here we report the structural characterization of the PilF TFP assembly ATPase from Thermus thermophilus. The crystal structure of a recombinant C-terminal fragment of PilF revealed bound, unhydrolysed ATP, although the full length complex was enzymatically active. 3D reconstructions were carried out by single particle cryoelectron microscopy for full length apoprotein PilF and in complex with AMPPNP. The structure forms an hourglass-like shape, with the ATPase domains in one half and the N1 domains in the second half which, we propose, interact with the other pilus biogenesis components. Molecular models for both forms were generated: binding of AMPPNP causes an upward shift of the N1 domains towards the ATPase domains of ~8 Å. We advocate a model in which ATP hydrolysis is linked to displacement of the N1 domains which is associated with lifting pilin subunits out of the inner membrane, and provide the activation energy needed to form the pilus fiber. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 457 KB | Display | ![]() |
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PDB format | ![]() | 374.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3882C ![]() 4194C ![]() 6ejfC ![]() 6f8lC ![]() 2gszS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein , 1 types, 6 molecules ABCDEF
#1: Protein | Mass: 43126.621 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 5 types, 409 molecules ![](data/chem/img/ATP.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-ATP / #3: Chemical | ChemComp-MG / #4: Chemical | ChemComp-ZN / #5: Chemical | ChemComp-CL / #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.91 Å3/Da / Density % sol: 57.72 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop Details: 0.2 M Sodium bromide, 0.1 M Bis-Tris propane pH 6.5, 20 % (w/v) PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 7, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.072 Å / Relative weight: 1 |
Reflection | Resolution: 2.44→95.106 Å / Num. obs: 109033 / % possible obs: 98.8 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.104 / Net I/σ(I): 11.5 |
Reflection shell | Resolution: 2.44→2.5 Å |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2GSZ Resolution: 2.44→95.106 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.26 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.44→95.106 Å
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Refine LS restraints |
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LS refinement shell |
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