3BWU | pdb_00003bwu

Crystal structure of the ternary complex of FimD (N-Terminal Domain, FimDN) with FimC and the N-terminally truncated pilus subunit FimF (FimFt)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.76 Å
  • R-Value Free: 
    0.212 (Depositor), 0.211 (DCC) 
  • R-Value Work: 
    0.175 (Depositor), 0.172 (DCC) 

Starting Model: experimental
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This is version 1.4 of the entry. See complete history. 

Literature

Crystal structure of the ternary FimC-FimF(t)-FimD(N) complex indicates conserved pilus chaperone-subunit complex recognition by the usher FimD

Eidam, O., Dworkowski, F.S., Glockshuber, R., Grutter, M.G., Capitani, G.

(2008) FEBS Lett 582: 651-655

  • DOI: https://doi.org/10.1016/j.febslet.2008.01.030
  • Primary Citation Related Structures: 
    3BWU

  • PubMed Abstract: 

    Type 1 pili, anchored to the outer membrane protein FimD, enable uropathogenic Escherichia coli to attach to host cells. During pilus biogenesis, the N-terminal periplasmic domain of FimD (FimD(N)) binds complexes between the chaperone FimC and pilus subunits via its partly disordered N-terminal segment, as recently shown for the FimC-FimH(P)-FimD(N) ternary complex. We report the structure of a new ternary complex (FimC-FimF(t)-FimD(N)) with the subunit FimF(t) instead of FimH(p). FimD(N) recognizes FimC-FimF(t) and FimC-FimH(P) very similarly, predominantly through hydrophobic interactions. The conserved binding mode at a "hot spot" on the chaperone surface could guide the design of pilus assembly inhibitors.

    • Organizational Affiliation: 
    • University of Zurich, Department of Biochemistry, Winterthurerstrasse 190, Zurich, Switzerland.

Macromolecule Content 

  • Total Structure Weight: 52.17 kDa 
  • Atom Count: 4,210 
  • Modeled Residue Count: 449 
  • Deposited Residue Count: 472 
  • Unique protein chains: 3

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Chaperone protein fimCA [auth C]205Escherichia coli K-12Mutation(s): 0 
Gene Names: fimC
UniProt
Find proteins for P31697 (Escherichia coli (strain K12))
Explore P31697 
Go to UniProtKB:  P31697
Entity Groups
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UniProt GroupP31697
Sequence Annotations
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Reference Sequence
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|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Outer membrane usher protein FimD, N-terminal domainB [auth D]125Escherichia coli K-12Mutation(s): 0 
Gene Names: fimD
UniProt
Find proteins for P30130 (Escherichia coli (strain K12))
Explore P30130 
Go to UniProtKB:  P30130
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UniProt GroupP30130
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Reference Sequence
Find similar proteins by:
|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Protein fimFC [auth F]142Escherichia coli K-12Mutation(s): 0 
Gene Names: fimF
UniProt
Find proteins for P08189 (Escherichia coli (strain K12))
Explore P08189 
Go to UniProtKB:  P08189
Entity Groups
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UniProt GroupP08189
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PEG

Query on PEG


Download:Ideal Coordinates CCD File
L [auth C]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
EDO

Query on EDO


Download:Ideal Coordinates CCD File
D [auth C]
E [auth C]
F [auth C]
G [auth C]
H [auth C]
D [auth C],
E [auth C],
F [auth C],
G [auth C],
H [auth C],
I [auth C],
J [auth C],
K [auth C],
M [auth D],
N [auth D],
O [auth F],
P [auth F],
Q [auth F]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.76 Å
  • R-Value Free:  0.212 (Depositor), 0.211 (DCC) 
  • R-Value Work:  0.175 (Depositor), 0.172 (DCC) 
Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 126.948α = 90
b = 126.948β = 90
c = 68.755γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
SLS-specificdata collection
HKL-2000data reduction
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-03-04
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Source and taxonomy, Version format compliance
  • Version 1.2: 2017-10-25
    Changes: Advisory, Refinement description
  • Version 1.3: 2023-08-30
    Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description
  • Version 1.4: 2024-11-20
    Changes: Structure summary