8PSV | pdb_00008psv

2.7 A cryo-EM structure of in vitro assembled type 1 pilus rod

• PDB DOI: https://doi.org/10.2210/pdb8PSV/pdb
• EM Map EMD-17863: EMDB EMDataResource

• Classification: STRUCTURAL PROTEIN
• Organism(s): Escherichia coli
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2023-07-13 Released: 2024-04-10 
• Deposition Author(s): Hospenthal, M., Zyla, D., Glockshuber, R., Waksman, G.
• Funding Organization(s): Swiss National Science Foundation, Medical Research Council (MRC, United Kingdom)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.70 Å
• Aggregation State: FILAMENT 
• Reconstruction Method: HELICAL 

Starting Model: experimental

Literature

The assembly platform FimD is required to obtain the most stable quaternary structure of type 1 pili.

Zyla, D.S., Wiegand, T., Bachmann, P., Zdanowicz, R., Giese, C., Meier, B.H., Waksman, G., Hospenthal, M.K., Glockshuber, R.

(2024) Nat Commun 15: 3032-3032

• PubMed: 38589417 
• DOI: https://doi.org/10.1038/s41467-024-47212-9
• Primary Citation Related Structures: 
  6Y7S, 8PSV, 8PTU


• PubMed Abstract: 
  

  Type 1 pili are important virulence factors of uropathogenic Escherichia coli that mediate bacterial attachment to epithelial cells in the urinary tract. The pilus rod is comprised of thousands of copies of the main structural subunit FimA and is assembled in vivo by the assembly platform FimD. Although type 1 pilus rods can self-assemble from FimA in vitro, this reaction is slower and produces structures with lower kinetic stability against denaturants compared to in vivo-assembled rods. Our study reveals that FimD-catalysed in vitro-assembled type 1 pilus rods attain a similar stability as pilus rods assembled in vivo. Employing structural, biophysical and biochemical analyses, we show that in vitro assembly reactions lacking FimD produce pilus rods with structural defects, reducing their stability against dissociation. Overall, our results indicate that FimD is not only required for the catalysis of pilus assembly, but also to control the assembly of the most stable quaternary structure.

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Organizational Affiliation: 
• Institute of Molecular Biology and Biophysics, ETH Zürich, Otto-Stern-Weg 5, 8093, Zürich, Switzerland.
La Jolla Institute for Immunology, 9420 Athena Cir, La Jolla, CA, 92037, USA.
Laboratory of Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 1-5/10, 8093, Zürich, Switzerland.
Institute of Technical and Macromolecular Chemistry, RWTH Aachen University, Worringerweg 2, 52074, Aachen, Germany.
Max Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, 45470, Mülheim/Ruhr, Germany.
Institute of Structural and Molecular Biology, University College London and Birkbeck, London, WC1E 7HX, UK.
Institute of Molecular Biology and Biophysics, ETH Zürich, Otto-Stern-Weg 5, 8093, Zürich, Switzerland. [e-mail].
Institute of Structural and Molecular Biology, University College London and Birkbeck, London, WC1E 7HX, UK. [e-mail].

Biological Assembly 1  

Global Symmetry: Helical - H  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 108.73 kDa 
• Atom Count: 6,642 
• Modeled Residue Count: 948 
• Deposited Residue Count: 1,092 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Type-1 fimbrial protein, A chain	A, B, C, D, E, F	182	Escherichia coli	Mutation(s): 0  Gene Names: fimA, pilA, b4314, JW4277
UniProt
Find proteins for P04128 (Escherichia coli (strain K12)) Explore P04128  Go to UniProtKB:  P04128

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.70 Å
• Aggregation State: FILAMENT 
• Reconstruction Method: HELICAL 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION	3.08
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-04-10 
Deposition Author(s): Hospenthal, M., Zyla, D., Glockshuber, R., Waksman, G.

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Funding Organization	Location	Grant Number
Swiss National Science Foundation	Switzerland	310030B_176403/1
Swiss National Science Foundation	Switzerland	31003A_156304
Swiss National Science Foundation	Switzerland	310030_201234
Medical Research Council (MRC, United Kingdom)	United Kingdom	018434

Revision History  

• Version 1.0: 2024-04-10
  Type: Initial release
  
• Version 1.1: 2024-04-17
  Changes: Database references
• Version 1.2: 2024-11-13
  Changes: Data collection, Structure summary