6V1C

Crystal structure of human trefoil factor 3 in complex with its cognate ligand

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.174 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history. 


Literature

Trefoil factors share a lectin activity that defines their role in mucus.

Jarva, M.A., Lingford, J.P., John, A., Soler, N.M., Scott, N.E., Goddard-Borger, E.D.

(2020) Nat Commun 11: 2265-2265

  • DOI: 10.1038/s41467-020-16223-7
  • Primary Citation of Related Structures:  
    6V1D, 6V1C

  • PubMed Abstract: 

    • The mucosal epithelium secretes a host of protective disulfide-rich peptides, including the trefoil factors (TFFs). The TFFs increase the viscoelasticity of the mucosa and promote cell migration, though the molecular mechanisms underlying these functions have remained poorly defined ...

    The mucosal epithelium secretes a host of protective disulfide-rich peptides, including the trefoil factors (TFFs). The TFFs increase the viscoelasticity of the mucosa and promote cell migration, though the molecular mechanisms underlying these functions have remained poorly defined. Here, we demonstrate that all TFFs are divalent lectins that recognise the GlcNAc-α-1,4-Gal disaccharide, which terminates some mucin-like O-glycans. Degradation of this disaccharide by a glycoside hydrolase abrogates TFF binding to mucins. Structural, mutagenic and biophysical data provide insights into how the TFFs recognise this disaccharide and rationalise their ability to modulate the physical properties of mucus across different pH ranges. These data reveal that TFF activity is dependent on the glycosylation state of mucosal glycoproteins and alludes to a lectin function for trefoil domains in other human proteins.

    Organizational Affiliation: 

    Department of Medical Biology, University of Melbourne, Parkville, VIC, 3010, Australia. goddard-borger.e@wehi.edu.au.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Trefoil factor 3 A61Homo sapiensMutation(s): 1 
Gene Names: TFF3, ITF, TFI
Find proteins for Q07654 (Homo sapiens)
Explore Q07654 
Go to UniProtKB:  Q07654
NIH Common Fund Data Resources
PHAROS:  Q07654
GTEx:  ENSG00000160180
Protein Feature View
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-beta-D-galactopyranose
B
2 N/A Oligosaccharides Interaction
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MLY
Query on MLY		AL-PEPTIDE LINKINGC8 H18 N2 O2LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.174 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 37.588α = 90
b = 37.588β = 90
c = 87.48γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Health and Medical Research Council (NHMRC, Australia)AustraliaGNT1139549

Revision History  (Full details and data files)

  • Version 1.0: 2019-12-11
    Type: Initial release
  • Version 1.1: 2020-05-27
    Changes: Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Author supporting evidence, Data collection, Derived calculations, Non-polymer description, Structure summary