6E14

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


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 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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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Type 1 fimbrin D-mannose specific adhesinH300Escherichia coliMutation(s): 0 
Gene Names: fimHb4320JW4283
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
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_3APZ14_00735AW106_26365COD30_02575CXB56_24500ERS085374_04437ERS150876_04614FORC28_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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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Protein FimFF156Escherichia coliMutation(s): 0 
Gene Names: fimFb4318JW4281
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
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Protein FimGG158Escherichia coliMutation(s): 0 
Gene Names: fimGb4319JW4282
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))
Explore P08190 
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Chaperone protein FimCC241Escherichia coliMutation(s): 0 
Gene Names: fimCb4316JW4279
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
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.00 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: 2019-12-18
    Changes: Author supporting evidence