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: 26.04 kDa 
• Atom Count: 1848 
• Modelled Residue Count: 216 
• Deposited Residue Count: 229 
• Unique protein chains: 1

5TGK

Nucleotide-binding domain 1 of the human cystic fibrosis transmembrane conductance regulator (CFTR) with dATP

• DOI: 10.2210/pdb5TGK/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): Yes 


• Deposited: 2016-09-28 Released: 2018-05-09 
• Deposition Author(s): Wang, C., Aleksandrov, A.A., Yang, Z., Forouhar, F., Proctor, E., Kota, P., An, J., Kaplan, A., Khazanov, N., Boel, G., Stockwell, B.R., Senderowitz, H., Dokholyan, N.V., Riordan, J.R., Brouillette, C.G., Hunt, J.F.
• Funding Organization(s): Cystic Fibrosis Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.91 Å
• R-Value Free: 0.198 
• R-Value Work: 0.155 
• R-Value Observed: 0.159 

Literature

Ligand binding to a remote site thermodynamically corrects the F508del mutation in the human cystic fibrosis transmembrane conductance regulator.

Wang, C., Aleksandrov, A.A., Yang, Z., Forouhar, F., Proctor, E.A., Kota, P., An, J., Kaplan, A., Khazanov, N., Boel, G., Stockwell, B.R., Senderowitz, H., Dokholyan, N.V., Riordan, J.R., Brouillette, C.G., Hunt, J.F.

(2018) J Biol Chem 

• PubMed: 29903914 
• DOI: 10.1074/jbc.RA117.000819
• Primary Citation of Related Structures:  
  5TGK


• PubMed Abstract: 
  

Many disease-causing mutations impair protein stability. Here, we explore a thermodynamic strategy to correct the disease-causing F508del mutation in the human cystic fibrosis transmembrane conductance regulator (hCFTR). F508del destabilizes nucleotide-binding domain 1 (hNBD1) in hCFTR relative to an aggregation-prone intermediate. We developed a fluorescence self-quenching assay for compounds that prevent aggregation of hNBD1 by stabilizing its native conformation. Unexpectedly, we found that dTTP and nucleotide analogs with exocyclic methyl groups bind to hNBD1 more strongly than ATP and preserve electrophysiological function of full-length F508del-hCFTR channels at temperatures up to 37 °C. Furthermore, nucleotides that increase open-channel probability, which reflects stabilization of an interdomain interface to hNBD1, thermally protect full-length F508del-hCFTR even when they do not stabilize isolated hNBD1. Therefore, stabilization of hNBD1 itself or of one of its interdomain interfaces by a small molecule indirectly offsets the destabilizing effect of the F508del mutation on full-length hCFTR. These results indicate that high-affinity binding of a small molecule to a remote site can correct a disease-causing mutation. We propose that the strategies described here should be applicable to identifying small molecules to help manage other human diseases caused by mutations that destabilize native protein conformation.

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Organizational Affiliation: 

From the Departments of Biological Sciences and [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cystic fibrosis transmembrane conductance regulator	A	229	Homo sapiens	Mutation(s): 1  Gene Names: CFTR, ABCC7 EC: 3.6.3.49 (PDB Primary Data), 5.6.1.6 (UniProt)
Find proteins for P13569 (Homo sapiens) Explore P13569  Go to UniProtKB:  P13569
NIH Common Fund Data Resources
PHAROS:  P13569 GTEx:  ENSG00000001626

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DTP	A	2'-DEOXYADENOSINE 5'-TRIPHOSPHATE C10 H16 N5 O12 P3 SUYVUBYJARFZHO-RRKCRQDMSA-N
MG	A	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.91 Å
• R-Value Free: 0.198 
• R-Value Work: 0.155 
• R-Value Observed: 0.159 
• Space Group: P 4₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.16	α = 90
b = 40.16	β = 90
c = 141.775	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data scaling

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2016-09-28 
• Released Date: 2018-05-09 
Deposition Author(s): Wang, C., Aleksandrov, A.A., Yang, Z., Forouhar, F., Proctor, E., Kota, P., An, J., Kaplan, A., Khazanov, N., Boel, G., Stockwell, B.R., Senderowitz, H., Dokholyan, N.V., Riordan, J.R., Brouillette, C.G., Hunt, J.F.

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Funding Organization	Location	Grant Number
Cystic Fibrosis Foundation	United States	Hunt13XX0

Revision History  

• Version 1.0: 2018-05-09
  Type: Initial release
  
• Version 1.1: 2018-06-27
  Changes: Data collection, Database references