9E9G | pdb_00009e9g

Heligmosomoides polygyrus TGF-beta Mimic 6 Domain 3 (TGM6-D3) Bound to Human TGF-beta Type II Receptor Extracellular Domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 
    0.182 (Depositor), 0.183 (DCC) 
  • R-Value Work: 
    0.160 (Depositor), 0.160 (DCC) 
  • R-Value Observed: 
    0.161 (Depositor) 

Starting Models: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

TGM6 is a helminth secretory product that mimics TGF-beta binding to TGFBR2 to antagonize signaling in fibroblasts.

White, S.E.Schwartze, T.A.Mukundan, A.Schoenherr, C.Singh, S.P.van Dinther, M.Cunningham, K.T.White, M.P.J.Campion, T.Pritchard, J.Hinck, C.S.Ten Dijke, P.Inman, G.J.Maizels, R.M.Hinck, A.P.

(2025) Nat Commun 16: 1847-1847

  • DOI: https://doi.org/10.1038/s41467-025-56954-z
  • Primary Citation of Related Structures:  
    9E9G

  • PubMed Abstract: 

    TGM6 is a natural antagonist of mammalian TGF-β signaling produced by the murine helminth parasite Heligmosomoides polygyrus. It differs from the previously described agonist, TGM1 (TGF-β Mimic-1), in that it lacks domains 1/2 that bind TGFBR1. It nonetheless retains TGFBR2 binding through domain 3 and potently inhibits TGF-β signaling in fibroblasts and epithelial cells, but does not inhibit TGF-β signaling in T cells, consistent with divergent domains 4/5 and an altered co-receptor binding preference. The crystal structure of TGM6 bound to TGFBR2 reveals an interface remarkably similar to that of TGF-β with TGFBR2. Thus, TGM6 has adapted its structure to mimic TGF-β, while engaging a distinct co-receptor to direct antagonism to fibroblasts and epithelial cells. The co-expression of TGM6, along with immunosuppressive TGMs that activate the TGF-β pathway, may minimize fibrotic damage to the host as the parasite progresses through its life cycle from the intestinal lumen to submucosa and back again. The co-receptor-dependent targeting of TGFBR2 by the parasite provides a template for the development of therapies for targeting the cancer- and fibrosis-promoting activities of the TGF-βs in humans.


  • Organizational Affiliation
    • Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
TGF-beta receptor type-2118Homo sapiensMutation(s): 0 
Gene Names: TGFBR2
EC: 2.7.11.30
UniProt & NIH Common Fund Data Resources
Find proteins for P37173 (Homo sapiens)
Explore P37173 
Go to UniProtKB:  P37173
PHAROS:  P37173
GTEx:  ENSG00000163513 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP37173
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Transforming growth factor beta mimic 692Heligmosomoides polygyrusMutation(s): 0 
UniProt
Find proteins for A0A2P1IQ80 (Heligmosomoides polygyrus bakeri)
Explore A0A2P1IQ80 
Go to UniProtKB:  A0A2P1IQ80
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A2P1IQ80
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CAC
Query on CAC

Download Ideal Coordinates CCD File 
N [auth A],
O [auth A]
CACODYLATE ION
C2 H6 As O2
OGGXGZAMXPVRFZ-UHFFFAOYSA-M
GOL
Query on GOL

Download Ideal Coordinates CCD File 
C [auth A]
D [auth A]
E [auth A]
F [auth A]
G [auth A]
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
P [auth B],
Q [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
I [auth A],
R [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA
Query on NA

Download Ideal Coordinates CCD File 
J [auth A],
K [auth A],
L [auth A],
M [auth A],
S [auth B]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free:  0.182 (Depositor), 0.183 (DCC) 
  • R-Value Work:  0.160 (Depositor), 0.160 (DCC) 
  • R-Value Observed: 0.161 (Depositor) 
Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.042α = 90
b = 128.387β = 90
c = 29.654γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM088119
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI153915

Revision History  (Full details and data files)

  • Version 1.0: 2025-01-22
    Type: Initial release
  • Version 1.1: 2025-08-06
    Changes: Database references