6O2P | pdb_00006o2p

Complex of ivacaftor with cystic fibrosis transmembrane conductance regulator (CFTR)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 6O2P

This is version 2.1 of the entry. See complete history

Literature

Structural identification of a hotspot on CFTR for potentiation.

Liu, F.Zhang, Z.Levit, A.Levring, J.Touhara, K.K.Shoichet, B.K.Chen, J.

(2019) Science 364: 1184-1188

  • DOI: https://doi.org/10.1126/science.aaw7611
  • Primary Citation Related Structures: 
    6O1V, 6O2P

  • PubMed Abstract: 

    Cystic fibrosis is a fatal disease caused by mutations in the cystic fibrosis transmembrane conductance regulator (CFTR). Two main categories of drugs are being developed: correctors that improve folding of CFTR and potentiators that recover the function of CFTR. Here, we report two cryo-electron microscopy structures of human CFTR in complex with potentiators: one with the U.S. Food and Drug Administration (FDA)-approved drug ivacaftor at 3.3-angstrom resolution and the other with an investigational drug, GLPG1837, at 3.2-angstrom resolution. These two drugs, although chemically dissimilar, bind to the same site within the transmembrane region. Mutagenesis suggests that in both cases, hydrogen bonds provided by the protein are important for drug recognition. The molecular details of how ivacaftor and GLPG1837 interact with CFTR may facilitate structure-based optimization of therapeutic compounds.


  • Organizational Affiliation
    • Laboratory of Membrane Biophysics and Biology, The Rockefeller University, New York, NY 10065, USA.

Macromolecule Content 

  • Total Structure Weight: 178.06 kDa 
  • Atom Count: 9,767 
  • Modeled Residue Count: 1,196 
  • Deposited Residue Count: 1,506 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Cystic fibrosis transmembrane conductance regulator1,489Homo sapiensMutation(s): 1 
Gene Names: CFTRABCC7
EC: 3.6.3.49 (PDB Primary Data), 5.6.1.6 (UniProt)
Membrane Entity: Yes 
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:  Sequence   |   3D Structure  
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Unknown Peptide17Homo sapiensMutation(s): 0 

Small Molecules

Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
AJP

Query on AJP



Download:Ideal Coordinates CCD File
M [auth A]Digitonin
C56 H92 O29
UVYVLBIGDKGWPX-KUAJCENISA-N
POV

Query on POV



Download:Ideal Coordinates CCD File
G [auth A]
H [auth A]
I [auth A]
J [auth A]
K [auth A]
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A]
(2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
C42 H82 N O8 P
WTJKGGKOPKCXLL-PFDVCBLKSA-N
ATP

Query on ATP



Download:Ideal Coordinates CCD File
E [auth A],
F [auth A]
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
VX7

Query on VX7



Download:Ideal Coordinates CCD File
N [auth A]N-(2,4-di-tert-butyl-5-hydroxyphenyl)-4-oxo-1,4-dihydroquinoline-3-carboxamide
C24 H28 N2 O3
PURKAOJPTOLRMP-UHFFFAOYSA-N
MG

Query on MG



Download:Ideal Coordinates CCD File
C [auth A],
D [auth A]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
VX7 BindingDB:  6O2P EC50: min: 3, max: 236 (nM) from 12 assay(s)

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTREFMAC
RECONSTRUCTIONFREALIGN

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Howard Hughes Medical Institute (HHMI)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2019-06-26
    Type: Initial release
  • Version 1.1: 2019-07-03
    Changes: Data collection, Database references
  • Version 1.2: 2019-11-20
    Changes: Author supporting evidence
  • Version 1.3: 2019-11-27
    Changes: Data collection
  • Version 2.0: 2021-08-25
    Changes: Advisory, Atomic model, Data collection, Database references
  • Version 2.1: 2024-05-15
    Changes: Data collection, Refinement description