1R0X

Cystic fibrosis transmembrane conductance regulator (CFTR) nucleotide-binding domain one (NBD1) with ATP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.234 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Structure of nucleotide-binding domain 1 of the cystic fibrosis transmembrane conductance regulator.

Lewis, H.A.Buchanan, S.G.Burley, S.K.Conners, K.Dickey, M.Dorwart, M.Fowler, R.Gao, X.Guggino, W.B.Hendrickson, W.A.Hunt, J.F.Kearins, M.C.Lorimer, D.Maloney, P.C.Post, K.W.Rajashankar, K.R.Rutter, M.E.Sauder, J.M.Shriver, S.Thibodeau, P.H.Thomas, P.J.Zhang, M.Zhao, X.Emtage, S.

(2004) EMBO J 23: 282-293

  • DOI: 10.1038/sj.emboj.7600040
  • Primary Citation of Related Structures:  
    1Q3H, 1R0W, 1R0X, 1R0Y, 1R0Z, 1R10

  • PubMed Abstract: 
  • Cystic fibrosis transmembrane conductance regulator (CFTR) is an ATP-binding cassette (ABC) transporter that functions as a chloride channel. Nucleotide-binding domain 1 (NBD1), one of two ABC domains in CFTR, also contains sites for the predominant CF-causing mutation and, potentially, for regulatory phosphorylation ...

    Cystic fibrosis transmembrane conductance regulator (CFTR) is an ATP-binding cassette (ABC) transporter that functions as a chloride channel. Nucleotide-binding domain 1 (NBD1), one of two ABC domains in CFTR, also contains sites for the predominant CF-causing mutation and, potentially, for regulatory phosphorylation. We have determined crystal structures for mouse NBD1 in unliganded, ADP- and ATP-bound states, with and without phosphorylation. This NBD1 differs from typical ABC domains in having added regulatory segments, a foreshortened subdomain interconnection, and an unusual nucleotide conformation. Moreover, isolated NBD1 has undetectable ATPase activity and its structure is essentially the same independent of ligand state. Phe508, which is commonly deleted in CF, is exposed at a putative NBD1-transmembrane interface. Our results are consistent with a CFTR mechanism, whereby channel gating occurs through ATP binding in an NBD1-NBD2 nucleotide sandwich that forms upon displacement of NBD1 regulatory segments.


    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Cystic fibrosis transmembrane conductance regulatorA, B, C, D286Mus musculusMutation(s): 0 
Gene Names: CFTR OR ABCC7CftrAbcc7
EC: 5.6.1.6
UniProt
Find proteins for P26361 (Mus musculus)
Explore P26361 
Go to UniProtKB:  P26361
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ATP (Subject of Investigation/LOI)
Query on ATP

Download Ideal Coordinates CCD File 
F [auth A], J [auth B], M [auth C], P [auth D]ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
 Ligand Interaction
ACY
Query on ACY

Download Ideal Coordinates CCD File 
G [auth A], H [auth A], K [auth B], N [auth C], Q [auth D], R [auth D]ACETIC ACID
C2 H4 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
E [auth A], I [auth B], L [auth C], O [auth D]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
ATP Binding MOAD:  1R0X Kd: 1.49e+5 (nM) from 1 assay(s)
PDBBind:  1R0X Kd: 1.49e+5 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.234 
  • Space Group: P 4 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 173.292α = 90
b = 173.292β = 90
c = 110.46γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
EPMRphasing
REFMACrefinement

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-12-09
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2021-02-03
    Changes: Database references, Derived calculations, Structure summary