5TX6 | pdb_00005tx6

Structure of TGF-beta2 derivative with deletion of residues 52-71 and 10 single amino acid mutations (mmTGF-beta2-7M)

• PDB DOI: https://doi.org/10.2210/pdb5TX6/pdb

• Classification: CYTOKINE
• Organism(s): Mus musculus
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2016-11-15 Released: 2017-03-01 
• Deposition Author(s): Petrunak, E.M., Hinck, A.P.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Cancer Institute (NIH/NCI), Robert A. Welch Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.75 Å
• R-Value Free: 
  0.272 (Depositor), 0.272 (DCC) 
• R-Value Work: 
  0.213 (Depositor), 0.217 (DCC) 
• R-Value Observed: 
  0.216 (Depositor) 

Starting Model: experimental

Literature

An engineered transforming growth factor beta (TGF-beta ) monomer that functions as a dominant negative to block TGF-beta signaling.

Kim, S.K., Barron, L., Hinck, C.S., Petrunak, E.M., Cano, K.E., Thangirala, A., Iskra, B., Brothers, M., Vonberg, M., Leal, B., Richter, B., Kodali, R., Taylor, A.B., Du, S., Barnes, C.O., Sulea, T., Calero, G., Hart, P.J., Hart, M.J., Demeler, B., Hinck, A.P.

(2017) J Biological Chem 292: 7173-7188

• PubMed: 28228478 
• DOI: https://doi.org/10.1074/jbc.M116.768754
• Primary Citation Related Structures: 
  5TX2, 5TX4, 5TX6


• PubMed Abstract: 
  

  The transforming growth factor β isoforms, TGF-β1, -β2, and -β3, are small secreted homodimeric signaling proteins with essential roles in regulating the adaptive immune system and maintaining the extracellular matrix. However, dysregulation of the TGF-β pathway is responsible for promoting the progression of several human diseases, including cancer and fibrosis. Despite the known importance of TGF-βs in promoting disease progression, no inhibitors have been approved for use in humans. Herein, we describe an engineered TGF-β monomer, lacking the heel helix, a structural motif essential for binding the TGF-β type I receptor (TβRI) but dispensable for binding the other receptor required for TGF-β signaling, the TGF-β type II receptor (TβRII), as an alternative therapeutic modality for blocking TGF-β signaling in humans. As shown through binding studies and crystallography, the engineered monomer retained the same overall structure of native TGF-β monomers and bound TβRII in an identical manner. Cell-based luciferase assays showed that the engineered monomer functioned as a dominant negative to inhibit TGF-β signaling with a K _i of 20-70 nm Investigation of the mechanism showed that the high affinity of the engineered monomer for TβRII, coupled with its reduced ability to non-covalently dimerize and its inability to bind and recruit TβRI, enabled it to bind endogenous TβRII but prevented it from binding and recruiting TβRI to form a signaling complex. Such engineered monomers provide a new avenue to probe and manipulate TGF-β signaling and may inform similar modifications of other TGF-β family members.

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Organizational Affiliation: 
• the Departments of Biochemistry and Structural Biology and.
Cell Systems and Anatomy.
From the Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15260.
the National Research Council, Human Health Therapeutics Portfolio, Montréal, Quebec H4P 2R2, Canada.
Center for Innovative Drug Discovery, University of Texas Health Science Center, San Antonio, Texas 78229-3900, and.
From the Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15260, [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 31.94 kDa 
• Atom Count: 2,150 
• Modeled Residue Count: 261 
• Deposited Residue Count: 279 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transforming growth factor beta-2	A [auth B], B [auth A], C	93	Mus musculus	Mutation(s): 10  Gene Names: Tgfb2
UniProt
Find proteins for P27090 (Mus musculus) Explore P27090  Go to UniProtKB:  P27090

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	D [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.75 Å
• R-Value Free:  0.272 (Depositor), 0.272 (DCC) 
• R-Value Work:  0.213 (Depositor), 0.217 (DCC) 
• R-Value Observed: 0.216 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.744	α = 90
b = 81.744	β = 90
c = 80.926	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
iMOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2017-03-01 
Deposition Author(s): Petrunak, E.M., Hinck, A.P.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM58670
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	CA172886
Robert A. Welch Foundation	United States	AQ1842

Revision History  

• Version 1.0: 2017-03-01
  Type: Initial release
  
• Version 1.1: 2017-03-08
  Changes: Database references
• Version 1.2: 2017-05-10
  Changes: Database references
• Version 1.3: 2017-09-27
  Changes: Author supporting evidence
• Version 1.4: 2019-12-04
  Changes: Author supporting evidence
• Version 1.5: 2024-10-09
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary