5TGK

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


Experimental Data Snapshot

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

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 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: https://doi.org/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.


  • Organizational Affiliation

    From the Departments of Biological Sciences.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cystic fibrosis transmembrane conductance regulator229Homo sapiensMutation(s): 1 
Gene Names: CFTRABCC7
EC: 3.6.3.49
UniProt & NIH Common Fund Data Resources
Find proteins for P13569 (Homo sapiens)
Explore P13569 
Go to UniProtKB:  P13569
PHAROS:  P13569
GTEx:  ENSG00000001626 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP13569
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DTP
Query on DTP

Download Ideal Coordinates CCD File 
C [auth A]2'-DEOXYADENOSINE 5'-TRIPHOSPHATE
C10 H16 N5 O12 P3
SUYVUBYJARFZHO-RRKCRQDMSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
B [auth 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 = 40.16α = 90
b = 40.16β = 90
c = 141.775γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Cystic Fibrosis FoundationUnited StatesHunt13XX0

Revision History  (Full details and data files)

  • Version 1.0: 2018-05-09
    Type: Initial release
  • Version 1.1: 2018-06-27
    Changes: Data collection, Database references
  • Version 1.2: 2023-10-04
    Changes: Data collection, Database references, Derived calculations, Refinement description