Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 12.96 kDa 
• Atom Count: 1006 
• Residue Count: 102 
• Unique protein chains: 1

4P7U

Extracellular domain of type II Transforming Growth Factor Beta receptor in complex with NDSB-201

• DOI: 10.2210/pdb4P7U/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2014-03-27 Released: 2015-06-24 
• Deposition Author(s): Wangkanont, K., Forest, K.T.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.206 
• R-Value Work: 0.171 
• R-Value Observed: 0.174 

Literature

The non-detergent sulfobetaine-201 acts as a pharmacological chaperone to promote folding and crystallization of the type II TGF-beta receptor extracellular domain.

Wangkanont, K., Forest, K.T., Kiessling, L.L.

(2015) Protein Expr Purif 115: 19-25

• PubMed: 26073093 
• DOI: 10.1016/j.pep.2015.06.001
• Primary Citation of Related Structures:  
  4P7U


• PubMed Abstract: 
  

The roles of the extracellular domain of type II TGF-β receptor (TBRII-ECD) in physiological processes ranging from development to cancer to wound healing render it an attractive target for exploration with chemical tools. For such applications, large amounts of active soluble protein are needed, but the yields of TBRII-ECD we obtained with current folding protocols were variable. To expedite the identification of alternative folding conditions, we developed an on-plate screen. This assay indicated that effective folding additives included the non-detergent sulfobetaine-201 (NDSB-201). Although NDSB-201 can facilitate protein folding, the mode by which it does so is poorly understood. We postulated that specific interactions between NDSB-201 and TBRII-ECD might be responsible. Analysis by X-ray crystallography indicates that the TBRII-ECD possesses a binding pocket for NDSB-201. The pyridinium group of the additive stacks with a phenylalanine side chain in the binding site. The ability of NDSB-201 to occupy a pocket on the protein provides a molecular mechanism for the additive's ability to minimize TBRII-ECD aggregation and stabilize the folded state. NDSB-201 also accelerates TBRII-ECD crystallization, suggesting it may serve as a useful crystallization additive for proteins refolded with it. Our results also suggest there is a site on TBRII-ECD that could be targeted by small-molecule modulators.

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Organizational Affiliation: 

Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706, United States; Department of Biochemistry, University of Wisconsin-Madison, 433 Babcock Dr., Madison, WI 53706, United States. Electronic address: [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TGF-beta receptor type-2	A	112	Homo sapiens	Mutation(s): 2  Gene Names: TGFBR2 EC: 2.7.11.30
Find proteins for P37173 (Homo sapiens) Explore P37173  Go to UniProtKB:  P37173
NIH Common Fund Data Resources
PHAROS  P37173 GTEx  ENSG00000163513

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
1PS	A	3-PYRIDINIUM-1-YLPROPANE-1-SULFONATE C8 H11 N O3 S REEBJQTUIJTGAL-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.206 
• R-Value Work: 0.171 
• R-Value Observed: 0.174 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 33.574	α = 90
b = 40.463	β = 90
c = 75.837	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
DENZO	data reduction
PDB_EXTRACT	data extraction
SCALEPACK	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2014-03-27 
• Released Date: 2015-06-24 
Deposition Author(s): Wangkanont, K., Forest, K.T.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM055984

Revision History 

• Version 1.0: 2015-06-24
  Type: Initial release
  
• Version 1.1: 2015-09-30
  Changes: Database references
• Version 1.2: 2017-09-13
  Changes: Author supporting evidence, Derived calculations, Refinement description
• Version 1.3: 2019-12-25
  Changes: Author supporting evidence