1XMJ

Crystal structure of human deltaF508 human NBD1 domain with ATP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.220 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Impact of the delta-F508 Mutation in First Nucleotide-binding Domain of Human Cystic Fibrosis Transmembrane Conductance Regulator on Domain Folding and Structure

Lewis, H.A.Zhao, X.Wang, C.Sauder, J.M.Rooney, I.Noland, B.W.Lorimer, D.Kearins, M.C.Conners, K.Condon, B.Maloney, P.C.Guggino, W.B.Hunt, J.F.Emtage, S.

(2005) J.Biol.Chem. 280: 1346-1353

  • DOI: 10.1074/jbc.M410968200
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Cystic fibrosis is caused by defects in the cystic fibrosis transmembrane conductance regulator (CFTR), commonly the deletion of residue Phe-508 (DeltaF508) in the first nucleotide-binding domain (NBD1), which results in a severe reduction in the pop ...

    Cystic fibrosis is caused by defects in the cystic fibrosis transmembrane conductance regulator (CFTR), commonly the deletion of residue Phe-508 (DeltaF508) in the first nucleotide-binding domain (NBD1), which results in a severe reduction in the population of functional channels at the epithelial cell surface. Previous studies employing incomplete NBD1 domains have attributed this to aberrant folding of DeltaF508 NBD1. We report structural and biophysical studies on complete human NBD1 domains, which fail to demonstrate significant changes of in vitro stability or folding kinetics in the presence or absence of the DeltaF508 mutation. Crystal structures show minimal changes in protein conformation but substantial changes in local surface topography at the site of the mutation, which is located in the region of NBD1 believed to interact with the first membrane spanning domain of CFTR. These results raise the possibility that the primary effect of DeltaF508 is a disruption of proper interdomain interactions at this site in CFTR rather than interference with the folding of NBD1. Interestingly, increases in the stability of NBD1 constructs are observed upon introduction of second-site mutations that suppress the trafficking defect caused by the DeltaF508 mutation, suggesting that these suppressors might function indirectly by improving the folding efficiency of NBD1 in the context of the full-length protein. The human NBD1 structures also solidify the understanding of CFTR regulation by showing that its two protein segments that can be phosphorylated both adopt multiple conformations that modulate access to the ATPase active site and functional interdomain interfaces.


    Organizational Affiliation

    Structural GenomiX, Inc., San Diego, California 92121, USA. hal_lewis@stromix.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cystic fibrosis transmembrane conductance regulator
A
290Homo sapiensMutation(s): 7 
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
ATP
Query on ATP

Download SDF File 
Download CCD File 
A
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-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: 2.3 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.220 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 59.793α = 90.00
b = 59.793β = 90.00
c = 144.398γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
MOLREPphasing
SCALEdata scaling
CCP4data scaling
SCALEdata reduction
MOSFLMdata reduction
TRUNCATEdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-11-09
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2018-11-14
    Type: Data collection, Structure summary