6E15

Handover mechanism of the growing pilus by the bacterial outer membrane usher FimD

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 5.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history. 


Literature

Handover mechanism of the growing pilus by the bacterial outer-membrane usher FimD.

Du, M., Yuan, Z., Yu, H., Henderson, N., Sarowar, S., Zhao, G., Werneburg, G.T., Thanassi, D.G., Li, H.

(2018) Nature 562: 444-447

  • DOI: 10.1038/s41586-018-0587-z
  • Primary Citation of Related Structures:  
    6E15, 6E14

  • PubMed Abstract: 

    • Pathogenic bacteria such as Escherichia coli assemble surface structures termed pili, or fimbriae, to mediate binding to host-cell receptors 1 . Type 1 pili are assembled via the conserved chaperone-usher pathway 2-5 . The outer ...

    Pathogenic bacteria such as Escherichia coli assemble surface structures termed pili, or fimbriae, to mediate binding to host-cell receptors 1 . Type 1 pili are assembled via the conserved chaperone-usher pathway 2-5 . The outer-membrane usher FimD recruits pilus subunits bound by the chaperone FimC via the periplasmic N-terminal domain of the usher. Subunit translocation through the β-barrel channel of the usher occurs at the two C-terminal domains (which we label CTD1 and CTD2) of this protein. How the chaperone-subunit complex bound to the N-terminal domain is handed over to the C-terminal domains, as well as the timing of subunit polymerization into the growing pilus, have previously been unclear. Here we use cryo-electron microscopy to capture a pilus assembly intermediate (FimD-FimC-FimF-FimG-FimH) in a conformation in which FimD is in the process of handing over the chaperone-bound end of the growing pilus to the C-terminal domains. In this structure, FimF has already polymerized with FimG, and the N-terminal domain of FimD swings over to bind CTD2; the N-terminal domain maintains contact with FimC-FimF, while at the same time permitting access to the C-terminal domains. FimD has an intrinsically disordered N-terminal tail that precedes the N-terminal domain. This N-terminal tail folds into a helical motif upon recruiting the FimC-subunit complex, but reorganizes into a loop to bind CTD2 during handover. Because both the N-terminal and C-terminal domains of FimD are bound to the end of the growing pilus, the structure further suggests a mechanism for stabilizing the assembly intermediate to prevent the pilus fibre diffusing away during the incorporation of thousands of subunits.

    Organizational Affiliation: 

    Structural Biology Program, Van Andel Research Institute, Grand Rapids, MI, USA. Huilin.Li@vai.org.



Macromolecules
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(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Chaperone protein FimCC241Escherichia coliMutation(s): 0 
Gene Names: fimC, b4316, JW4279
Membrane protein
Mpstruc		Group: 
TRANSMEMBRANE PROTEINS: BETA-BARREL		Sub Group: 
Beta-Barrel Membrane Proteins: Monomeric/Dimeric		Protein: 
P pilus assembly intermediate (FimD-FimC-FimF-FimG-FimH), conformer 1
Find proteins for P31697 (Escherichia coli (strain K12))
Explore P31697 
Go to UniProtKB:  P31697
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Fimbrial biogenesis outer membrane usher proteinD879Escherichia coliMutation(s): 0 
Gene Names: fimD_3, APZ14_00735, AW106_26365, COD30_02575, CXB56_24500, ERS085374_04437, ERS150876_04614, FORC28_5312
Membrane protein
Mpstruc		Group: 
TRANSMEMBRANE PROTEINS: BETA-BARREL		Sub Group: 
Beta-Barrel Membrane Proteins: Monomeric/Dimeric		Protein: 
P pilus assembly intermediate (FimD-FimC-FimF-FimG-FimH), conformer 1
Find proteins for P30130 (Escherichia coli (strain K12))
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Go to UniProtKB:  P30130
Protein Feature View
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Protein FimFF156Escherichia coliMutation(s): 0 
Gene Names: fimF, b4318, JW4281
Membrane protein
Mpstruc		Group: 
TRANSMEMBRANE PROTEINS: BETA-BARREL		Sub Group: 
Beta-Barrel Membrane Proteins: Monomeric/Dimeric		Protein: 
P pilus assembly intermediate (FimD-FimC-FimF-FimG-FimH), conformer 1
Find proteins for P08189 (Escherichia coli (strain K12))
Explore P08189 
Go to UniProtKB:  P08189
Protein Feature View
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Protein FimGG158Escherichia coliMutation(s): 0 
Gene Names: fimG, b4319, JW4282
Membrane protein
Mpstruc		Group: 
TRANSMEMBRANE PROTEINS: BETA-BARREL		Sub Group: 
Beta-Barrel Membrane Proteins: Monomeric/Dimeric		Protein: 
P pilus assembly intermediate (FimD-FimC-FimF-FimG-FimH), conformer 1
Find proteins for P08190 (Escherichia coli (strain K12))
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Type 1 fimbrin D-mannose specific adhesinH300Escherichia coliMutation(s): 0 
Gene Names: fimH, b4320, JW4283
Membrane protein
Mpstruc		Group: 
TRANSMEMBRANE PROTEINS: BETA-BARREL		Sub Group: 
Beta-Barrel Membrane Proteins: Monomeric/Dimeric		Protein: 
P pilus assembly intermediate (FimD-FimC-FimF-FimG-FimH), conformer 1
Find proteins for P08191 (Escherichia coli (strain K12))
Explore P08191 
Go to UniProtKB:  P08191
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 5.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)United StatesGM062987

Revision History 

  • Version 1.0: 2018-10-17
    Type: Initial release
  • Version 1.1: 2018-10-31
    Changes: Data collection, Database references
  • Version 1.2: 2019-05-22
    Changes: Data collection, Refinement description
  • Version 1.3: 2019-12-18
    Changes: Author supporting evidence, Other