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Open data
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Basic information
Entry | Database: PDB / ID: 5wda | ||||||||||||||||||||||||||||||||||||||||||
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Title | Structure of the PulG pseudopilus | ||||||||||||||||||||||||||||||||||||||||||
![]() | General secretion pathway protein G | ||||||||||||||||||||||||||||||||||||||||||
![]() | PROTEIN TRANSPORT / helical polymer / bacterial secretion / cryo-EM | ||||||||||||||||||||||||||||||||||||||||||
Function / homology | ![]() protein secretion by the type II secretion system / type II protein secretion system complex / membrane => GO:0016020 / plasma membrane Similarity search - Function | ||||||||||||||||||||||||||||||||||||||||||
Biological species | ![]() | ||||||||||||||||||||||||||||||||||||||||||
Method | ELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 5 Å | ||||||||||||||||||||||||||||||||||||||||||
![]() | Lopez-Castilla, A. / Thomassin, J.L. / Bardiaux, B. / Zheng, W. / Nivaskumar, M. / Yu, X. / Nilges, M. / Egelman, E.H. / Izadi-Pruneyre, N. / Francetic, O. | ||||||||||||||||||||||||||||||||||||||||||
Funding support | ![]() ![]()
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![]() | ![]() Title: Structure of the calcium-dependent type 2 secretion pseudopilus. Authors: Aracelys López-Castilla / Jenny-Lee Thomassin / Benjamin Bardiaux / Weili Zheng / Mangayarkarasi Nivaskumar / Xiong Yu / Michael Nilges / Edward H Egelman / Nadia Izadi-Pruneyre / Olivera Francetic / ![]() ![]() Abstract: Many Gram-negative bacteria use type 2 secretion systems (T2SSs) to secrete proteins involved in virulence and adaptation. Transport of folded proteins via T2SS nanomachines requires the assembly of ...Many Gram-negative bacteria use type 2 secretion systems (T2SSs) to secrete proteins involved in virulence and adaptation. Transport of folded proteins via T2SS nanomachines requires the assembly of inner membrane-anchored fibres called pseudopili. Although efficient pseudopilus assembly is essential for protein secretion, structure-based functional analyses are required to unravel the mechanistic link between these processes. Here, we report an atomic model for a T2SS pseudopilus from Klebsiella oxytoca, obtained by fitting the NMR structure of its calcium-bound subunit PulG into the ~5-Å-resolution cryo-electron microscopy reconstruction of assembled fibres. This structure reveals the comprehensive network of inter-subunit contacts and unexpected features, including a disordered central region of the PulG helical stem, and highly flexible C-terminal residues on the fibre surface. NMR, mutagenesis and functional analyses highlight the key role of calcium in PulG folding and stability. Fibre disassembly in the absence of calcium provides a basis for pseudopilus length control, essential for protein secretion, and supports the Archimedes screw model for the type 2 secretion mechanism. | ||||||||||||||||||||||||||||||||||||||||||
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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PDBx/mmCIF format | ![]() | 1005.1 KB | Display | ![]() |
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PDB format | ![]() | 854.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 8812MC ![]() 5o2yC C: citing same article ( M: map data used to model this data |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Components
#1: Protein | Mass: 14525.482 Da / Num. of mol.: 25 / Fragment: UNP residues 7-140 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-CA / Has protein modification | Y | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: FILAMENT / 3D reconstruction method: helical reconstruction |
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Sample preparation
Component | Name: PulG pseudopilus / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: all / Source: RECOMBINANT |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: ![]() |
Source (recombinant) | Organism: ![]() ![]() |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 20 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON II (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 1819 |
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Processing
Software | Name: PHENIX / Version: 1.11.1_2575: / Classification: refinement | ||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Helical symmerty | Angular rotation/subunit: 83.2 ° / Axial rise/subunit: 10.2 Å / Axial symmetry: C1 | ||||||||||||||||||||||||
3D reconstruction | Resolution: 5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 85619 / Algorithm: BACK PROJECTION / Symmetry type: HELICAL | ||||||||||||||||||||||||
Refine LS restraints |
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