6GKD | pdb_00006gkd

human NBD1 of CFTR in complex with nanobodies D12 and G3a


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.99 Å
  • R-Value Free: 
    0.235 (Depositor), 0.238 (DCC) 
  • R-Value Work: 
    0.204 (Depositor), 0.208 (DCC) 
  • R-Value Observed: 
    0.193 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 6GKD

Ligand Structure Quality Assessment 


This is version 2.1 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: https://doi.org/10.1038/s41467-019-10714-y
  • Primary Citation Related Structures: 
    6GJQ, 6GJS, 6GJU, 6GK4, 6GKD

  • 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 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
    • SFMB, Université Libre de Bruxelles (ULB), CP206/02, Boulevard du Triomphe, building BC, B-1050, Brussels, Belgium.

Macromolecule Content 

  • Total Structure Weight: 354.28 kDa 
  • Atom Count: 20,891 
  • Modeled Residue Count: 2,761 
  • Deposited Residue Count: 3,162 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Cystic fibrosis transmembrane conductance regulator229Homo sapiensMutation(s): 0 
Gene Names: CFTR
EC: 3.6.3.49 (PDB Primary Data), 5.6.1.6 (UniProt)
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
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Nanobody D12149Lama glamaMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Nanobody G3a149Lama glamaMutation(s): 0 

Oligosaccharides

Help  
Entity ID: 4
MoleculeChains Length2D Diagram GlycosylationD Interactions
alpha-D-fructofuranose-(2-1)-alpha-D-glucopyranoseS [auth D],
T [auth E],
U,
V,
W
2N/A
Glycosylation Resources
GlyTouCan: G49187ZK
GlyCosmos: G49187ZK

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ATP

Query on ATP



Download:Ideal Coordinates CCD File
AA [auth F]
EA [auth I]
GA [auth L]
IA [auth O]
MA [auth R]
AA [auth F],
EA [auth I],
GA [auth L],
IA [auth O],
MA [auth R],
X [auth A]
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
GOL

Query on GOL



Download:Ideal Coordinates CCD File
LA [auth O],
OA [auth T]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
MG

Query on MG



Download:Ideal Coordinates CCD File
BA [auth F]
CA [auth F]
DA [auth F]
FA [auth I]
HA [auth L]
BA [auth F],
CA [auth F],
DA [auth F],
FA [auth I],
HA [auth L],
JA [auth O],
KA [auth O],
NA [auth R],
Y [auth A],
Z [auth A]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.99 Å
  • R-Value Free:  0.235 (Depositor), 0.238 (DCC) 
  • R-Value Work:  0.204 (Depositor), 0.208 (DCC) 
  • R-Value Observed: 0.193 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 116.94α = 90
b = 146.83β = 90
c = 188.34γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
XDSdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2019-06-19
    Type: Initial release
  • Version 1.1: 2019-06-26
    Changes: Data collection, Database references
  • Version 1.2: 2019-08-21
    Changes: Data collection, Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
  • Version 2.1: 2024-11-06
    Changes: Data collection, Database references, Structure summary