5NWP | pdb_00005nwp

Crystal Structure of the Lectin Domain From the F17-like Adhesin, UclD


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.05 Å
  • R-Value Free: 
    0.143 (Depositor), 0.143 (DCC) 
  • R-Value Work: 
    0.117 (Depositor), 0.118 (DCC) 
  • R-Value Observed: 
    0.118 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 5NWP

This is version 1.3 of the entry. See complete history

Literature

Selective depletion of uropathogenic E. coli from the gut by a FimH antagonist.

Spaulding, C.N.Klein, R.D.Ruer, S.Kau, A.L.Schreiber, H.L.Cusumano, Z.T.Dodson, K.W.Pinkner, J.S.Fremont, D.H.Janetka, J.W.Remaut, H.Gordon, J.I.Hultgren, S.J.

(2017) Nature 546: 528-532

  • DOI: https://doi.org/10.1038/nature22972
  • Primary Citation Related Structures: 
    5NWP, 5VQ5

  • PubMed Abstract: 

    Urinary tract infections (UTIs) caused by uropathogenic Escherichia coli (UPEC) affect 150 million people annually. Despite effective antibiotic therapy, 30-50% of patients experience recurrent UTIs. In addition, the growing prevalence of UPEC that are resistant to last-line antibiotic treatments, and more recently to carbapenems and colistin, make UTI a prime example of the antibiotic-resistance crisis and emphasize the need for new approaches to treat and prevent bacterial infections. UPEC strains establish reservoirs in the gut from which they are shed in the faeces, and can colonize the periurethral area or vagina and subsequently ascend through the urethra to the urinary tract, where they cause UTIs. UPEC isolates encode up to 16 distinct chaperone-usher pathway pili, and each pilus type may enable colonization of a habitat in the host or environment. For example, the type 1 pilus adhesin FimH binds mannose on the bladder surface, and mediates colonization of the bladder. However, little is known about the mechanisms underlying UPEC persistence in the gut. Here, using a mouse model, we show that F17-like and type 1 pili promote intestinal colonization and show distinct binding to epithelial cells distributed along colonic crypts. Phylogenomic and structural analyses reveal that F17-like pili are closely related to pilus types carried by intestinal pathogens, but are restricted to extra-intestinal pathogenic E. coli. Moreover, we show that targeting FimH with M4284, a high-affinity inhibitory mannoside, reduces intestinal colonization of genetically diverse UPEC isolates, while simultaneously treating UTI, without notably disrupting the structural configuration of the gut microbiota. By selectively depleting intestinal UPEC reservoirs, mannosides could markedly reduce the rate of UTIs and recurrent UTIs.


  • Organizational Affiliation
    • Department of Molecular Microbiology, Washington University in St Louis, St Louis, Missouri 63110, USA.

Macromolecule Content 

  • Total Structure Weight: 43.07 kDa 
  • Atom Count: 3,753 
  • Modeled Residue Count: 394 
  • Deposited Residue Count: 406 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Adhesin
A, B
203Escherichia coliMutation(s): 0 
Gene Names: OK10_24545WM48_23800
UniProt
Find proteins for Q1R2V7 (Escherichia coli (strain UTI89 / UPEC))
Explore Q1R2V7 
Go to UniProtKB:  Q1R2V7
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ1R2V7
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4

Query on SO4



Download:Ideal Coordinates CCD File
C [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.05 Å
  • R-Value Free:  0.143 (Depositor), 0.143 (DCC) 
  • R-Value Work:  0.117 (Depositor), 0.118 (DCC) 
  • R-Value Observed: 0.118 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 30.089α = 90
b = 91.871β = 96.46
c = 64.932γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
SHELXDphasing

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
FWOBelgiumG030411N

Revision History  (Full details and data files)

  • Version 1.0: 2017-06-21
    Type: Initial release
  • Version 1.1: 2017-06-28
    Changes: Database references
  • Version 1.2: 2017-07-05
    Changes: Database references
  • Version 1.3: 2024-05-01
    Changes: Data collection, Database references, Refinement description