5TGK

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.912 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.155 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

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. --: --

  • DOI: 10.1074/jbc.RA117.000819

  • 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 nucleoti ...

    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.


    Organizational Affiliation

    Chemistry, Columbia University, New York, New York 10027.,From the Departments of Biological Sciences and jfh21@columbia.edu.,From the Departments of Biological Sciences and.,the Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina, Chapel Hill, North Carolina 27599.,the Department of Chemistry, Bar-Ilan University, Ramat-Gan 5290002, Israel.,the Department of Chemistry, University of Alabama, Birmingham, Alabama 35294, and.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cystic fibrosis transmembrane conductance regulator
A
229Homo sapiensMutation(s): 1 
Gene Names: CFTR (ABCC7)
Find proteins for P13569 (Homo sapiens)
Go to Gene View: CFTR
Go to UniProtKB:  P13569
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DTP
Query on DTP

Download SDF File 
Download CCD File 
A
2'-DEOXYADENOSINE 5'-TRIPHOSPHATE
C10 H16 N5 O12 P3
SUYVUBYJARFZHO-RRKCRQDMSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.912 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.155 
  • Space Group: P 43
Unit Cell:
Length (Å)Angle (°)
a = 40.160α = 90.00
b = 40.160β = 90.00
c = 141.775γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Cystic Fibrosis FoundationUnited StatesHunt13XX0

Revision History 

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