6GJS

Human NBD1 of CFTR in complex with nanobodies D12 and T4


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.177 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Domain-interface dynamics of CFTR revealed by stabilizing nanobodies.

Sigoillot, M.Overtus, M.Grodecka, M.Scholl, D.Garcia-Pino, A.Laeremans, T.He, L.Pardon, E.Hildebrandt, E.Urbatsch, I.Steyaert, J.Riordan, J.R.Govaerts, C.

(2019) Nat Commun 10: 2636-2636

  • DOI: 10.1038/s41467-019-10714-y
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The leading cause of cystic fibrosis (CF) is the deletion of phenylalanine 508 (F508del) in the first nucleotide-binding domain (NBD1) of the cystic fibrosis transmembrane conductance regulator (CFTR). The mutation affects the thermodynamic stability ...

    The leading cause of cystic fibrosis (CF) is the deletion of phenylalanine 508 (F508del) in the first nucleotide-binding domain (NBD1) of the cystic fibrosis transmembrane conductance regulator (CFTR). The mutation affects the thermodynamic stability of the domain and the integrity of the interface between NBD1 and the transmembrane domain leading to its clearance by the quality control system. Here, we develop nanobodies targeting NBD1 of human CFTR and demonstrate their ability to stabilize both isolated NBD1 and full-length protein. Crystal structures of NBD1-nanobody complexes provide an atomic description of the epitopes and reveal the molecular basis for stabilization. Furthermore, our data uncover a conformation of CFTR, involving detachment of NBD1 from the transmembrane domain, which contrast with the compact assembly observed in cryo-EM structures. This unexpected interface rearrangement is likely to have major relevance for CF pathogenesis but also for the normal function of CFTR and other ABC proteins.


    Organizational Affiliation

    VIB-VUB center for Structural Biology, VIB, Pleinlaan 2, B-1050, Brussels, Belgium.,Laboratoire de Microbiologie Moléculaire et Cellulaire, ULB CP300, rue des Professeurs Jeener et Brachet 12, B-6041, Charleroi, Belgium.,Department of Biochemistry and Biophysics and Cystic Fibrosis Center, University of North Carolina-Chapel Hill, Chapel Hill, NC, 27599, USA.,Structural Biology Brussels, Vrije Universiteit Brussel (VUB), Pleinlaan 2, B-1050, Brussels, Belgium.,SFMB, Université Libre de Bruxelles (ULB), CP206/02, Boulevard du Triomphe, building BC, B-1050, Brussels, Belgium. Cedric.Govaerts@ulb.ac.be.,Department of Cell Biology and Biochemistry and Center for Membrane Protein Research, Texas Tech University Health Sciences Center, 3601 4th Street, Stop 6540, Lubbock, TX, 79430, USA.,SFMB, Université Libre de Bruxelles (ULB), CP206/02, Boulevard du Triomphe, building BC, B-1050, Brussels, Belgium.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cystic fibrosis transmembrane conductance regulator
A
229Homo sapiensMutation(s): 0 
Gene Names: CFTR (ABCC7)
Find proteins for P13569 (Homo sapiens)
Go to Gene View: CFTR
Go to UniProtKB:  P13569
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Nanobody D12
B
149N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Nanobody T4
C
143N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
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: 1.95 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.177 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 152.200α = 90.00
b = 41.600β = 120.56
c = 99.300γ = 90.00
Software Package:
Software NamePurpose
XDSdata scaling
MOLREPphasing
BUSTERrefinement
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2019-06-26
    Type: Initial release