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PDBsum entry 1xmi
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Membrane protein, hydrolase
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PDB id
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1xmi
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Contents |
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* Residue conservation analysis
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PDB id:
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Membrane protein, hydrolase
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Title:
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Crystal structure of human f508a nbd1 domain with atp
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Structure:
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Cystic fibrosis transmembrane conductance regulator. Chain: a, b, c, d, e. Fragment: nucleotide binding domain one. Synonym: cftr. Camp- dependent chloride channel. Engineered: yes. Mutation: yes
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Source:
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Homo sapiens. Human. Organism_taxid: 9606. Gene: cftr. Expressed in: escherichia coli. Expression_system_taxid: 562.
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Biol. unit:
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Pentamer (from
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Resolution:
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2.25Å
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R-factor:
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0.232
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R-free:
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0.265
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Authors:
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H.A.Lewis,X.Zhao,C.Wang,J.M.Sauder,I.Rooney,B.W.Noland,D.Lorimer, M.C.Kearins,K.Conners,B.Condon,P.C.Maloney,W.B.Guggino,J.F.Hunt, S.Emtage,Structural Genomix
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Key ref:
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H.A.Lewis
et al.
(2005).
Impact of the deltaF508 mutation in first nucleotide-binding domain of human cystic fibrosis transmembrane conductance regulator on domain folding and structure.
J Biol Chem,
280,
1346-1353.
PubMed id:
DOI:
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Date:
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02-Oct-04
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Release date:
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09-Nov-04
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PROCHECK
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Headers
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References
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P13569
(CFTR_HUMAN) -
Cystic fibrosis transmembrane conductance regulator from Homo sapiens
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Seq: Struc:
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1480 a.a.
267 a.a.*
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Key: |
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PfamA domain |
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Secondary structure |
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CATH domain |
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*
PDB and UniProt seqs differ
at 5 residue positions (black
crosses)
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Enzyme class:
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E.C.5.6.1.6
- channel-conductance-controlling ATPase.
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Reaction:
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ATP + H2O + closed Cl- channel = ADP + phosphate + open Cl- channel
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ATP
Bound ligand (Het Group name = )
corresponds exactly
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+
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H2O
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+
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closed Cl(-) channel
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=
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ADP
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+
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phosphate
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+
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open Cl(-) channel
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Molecule diagrams generated from .mol files obtained from the
KEGG ftp site
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DOI no:
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J Biol Chem
280:1346-1353
(2005)
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PubMed id:
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Impact of the deltaF508 mutation in first nucleotide-binding domain of human cystic fibrosis transmembrane conductance regulator on domain folding and structure.
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H.A.Lewis,
X.Zhao,
C.Wang,
J.M.Sauder,
I.Rooney,
B.W.Noland,
D.Lorimer,
M.C.Kearins,
K.Conners,
B.Condon,
P.C.Maloney,
W.B.Guggino,
J.F.Hunt,
S.Emtage.
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ABSTRACT
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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.
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Selected figure(s)
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Figure 1.
FIG. 1. Comparison of NBD1 structures. A, sequence
alignment of human and mouse NBD1 with NBD domains from other
ABC transporters. Blue background, -strands; pink, -helices; purple, 3[10]
helices; gray, absence of density in the electron density map.
Numbering of the secondary structure elements for CFTR NBD1 is
indicated in shaded blocks in the top row. Bold blue indicates
residues with high sequence conservation in ABC domains, while
bold red indicates residues that have been mutated in forms of
hNBD1. Protein Data Bank ID codes are indicated in parentheses.
B, stereo pair of superimposed worm diagrams of NBD1 from CFTR.
Regions with conformational differences are shown in cyan for
hNBD1-2b-F508A (molecule E), blue for hNBD1-7a- F508,
and gold for mNBD1 (molecule B). Bound ATP is shown in wire
frame representation employing the same colors. The figure was
made using Spock (31).
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Figure 2.
FIG. 2. Local structure at the site of Phe-508 in NBD1 of
CFTR. A, stereo image of conformation of Phe-508 loop region in
mNBD1 (gold), hNBD1-2b-F508A (cyan), and hNBD1-7a- F508
(blue). B and C, worm diagrams of hNBD1-2b-F508A (B) and
hNBD1-7a- F508 (C). Residues
507-510 in B are modeled from the mNBD1 structure. The position
of Phe-508 is shown in green. Positions of residues 507 and 509
are shown in gold. Helices in are red, -strands are in blue. D
and E, surface properties of hNBD1-2b-F508A (D) and hNBD1-7a-
F508 (E) in same
orientations as in B and C. Residues 507-510 in hNBD1-2b-F508A
structure have been replaced with those from the mNBD1 structure
to provide an image representative of the wild-type human
protein. Residues are colored to indicate hydrophobic (green),
negatively charged (red), positively charge (blue), and neutral
(white) side chains. The "F " label indicates the side chain of
Phe-508, and "V " indicates the side chain of Val-510. White
worms indicate the position of the L-loop from BtuCD (residues
217-227 from PDB id 117v:A) after least squares alignment of the
ABC subdomain from its NBD
with that from hNBD1. The structural differences visible at the
right side of these images derives from a change in the
conformation of the helix 4C-helix 5 loop and is likely a
results of variation in packing contacts between the two crystal
structures. The figure was made using Spock (31).
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The above figures are
reprinted
by permission from the ASBMB:
J Biol Chem
(2005,
280,
1346-1353)
copyright 2005.
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Figures were
selected
by an automated process.
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Literature references that cite this PDB file's key reference
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PubMed id
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Reference
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A.Khushoo,
Z.Yang,
A.E.Johnson,
and
W.R.Skach
(2011).
Ligand-driven vectorial folding of ribosome-bound human CFTR NBD1.
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Mol Cell,
41,
682-692.
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E.Noy,
and
H.Senderowitz
(2011).
Combating Cystic Fibrosis: In Search for CF Transmembrane Conductance Regulator (CFTR) Modulators.
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ChemMedChem,
6,
243-251.
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C.Wang,
I.Protasevich,
Z.Yang,
D.Seehausen,
T.Skalak,
X.Zhao,
S.Atwell,
J.Spencer Emtage,
D.R.Wetmore,
C.G.Brouillette,
and
J.F.Hunt
(2010).
Integrated biophysical studies implicate partial unfolding of NBD1 of CFTR in the molecular pathogenesis of F508del cystic fibrosis.
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Protein Sci,
19,
1932-1947.
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G.Roy,
E.M.Chalfin,
A.Saxena,
and
X.Wang
(2010).
Interplay between ER exit code and domain conformation in CFTR misprocessing and rescue.
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Mol Biol Cell,
21,
597-609.
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H.Hoelen,
B.Kleizen,
A.Schmidt,
J.Richardson,
P.Charitou,
P.J.Thomas,
and
I.Braakman
(2010).
The primary folding defect and rescue of ΔF508 CFTR emerge during translation of the mutant domain.
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PLoS One,
5,
e15458.
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I.Protasevich,
Z.Yang,
C.Wang,
S.Atwell,
X.Zhao,
S.Emtage,
D.Wetmore,
J.F.Hunt,
and
C.G.Brouillette
(2010).
Thermal unfolding studies show the disease causing F508del mutation in CFTR thermodynamically destabilizes nucleotide-binding domain 1.
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Protein Sci,
19,
1917-1931.
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J.F.Collawn,
L.Fu,
and
Z.Bebok
(2010).
Targets for cystic fibrosis therapy: proteomic analysis and correction of mutant cystic fibrosis transmembrane conductance regulator.
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Expert Rev Proteomics,
7,
495-506.
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J.L.Kreindler
(2010).
Cystic fibrosis: exploiting its genetic basis in the hunt for new therapies.
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Pharmacol Ther,
125,
219-229.
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M.F.Tsai,
M.Li,
and
T.C.Hwang
(2010).
Stable ATP binding mediated by a partial NBD dimer of the CFTR chloride channel.
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J Gen Physiol,
135,
399-414.
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M.Haffke,
A.Menzel,
Y.Carius,
D.Jahn,
and
D.W.Heinz
(2010).
Structures of the nucleotide-binding domain of the human ABCB6 transporter and its complexes with nucleotides.
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Acta Crystallogr D Biol Crystallogr,
66,
979-987.
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PDB codes:
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O.Kalid,
M.Mense,
S.Fischman,
A.Shitrit,
H.Bihler,
E.Ben-Zeev,
N.Schutz,
N.Pedemonte,
P.J.Thomas,
R.J.Bridges,
D.R.Wetmore,
Y.Marantz,
and
H.Senderowitz
(2010).
Small molecule correctors of F508del-CFTR discovered by structure-based virtual screening.
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J Comput Aided Mol Des,
24,
971-991.
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S.Atwell,
C.G.Brouillette,
K.Conners,
S.Emtage,
T.Gheyi,
W.B.Guggino,
J.Hendle,
J.F.Hunt,
H.A.Lewis,
F.Lu,
I.I.Protasevich,
L.A.Rodgers,
R.Romero,
S.R.Wasserman,
P.C.Weber,
D.Wetmore,
F.F.Zhang,
and
X.Zhao
(2010).
Structures of a minimal human CFTR first nucleotide-binding domain as a monomer, head-to-tail homodimer, and pathogenic mutant.
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Protein Eng Des Sel,
23,
375-384.
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PDB codes:
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S.Naik,
I.Haque,
N.Degner,
B.Kornilayev,
G.Bomhoff,
J.Hodges,
A.A.Khorassani,
H.Katayama,
J.Morris,
J.Kelly,
J.Seed,
and
M.T.Fisher
(2010).
Identifying protein stabilizing ligands using GroEL.
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Biopolymers,
93,
237-251.
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T.W.Loo,
M.C.Bartlett,
and
D.M.Clarke
(2010).
The V510D suppressor mutation stabilizes DeltaF508-CFTR at the cell surface.
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Biochemistry,
49,
6352-6357.
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V.Kanelis,
R.P.Hudson,
P.H.Thibodeau,
P.J.Thomas,
and
J.D.Forman-Kay
(2010).
NMR evidence for differential phosphorylation-dependent interactions in WT and DeltaF508 CFTR.
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EMBO J,
29,
263-277.
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J.P.Mornon,
P.Lehn,
and
I.Callebaut
(2009).
Molecular models of the open and closed states of the whole human CFTR protein.
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Cell Mol Life Sci,
66,
3469-3486.
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K.Du,
and
G.L.Lukacs
(2009).
Cooperative assembly and misfolding of CFTR domains in vivo.
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Mol Biol Cell,
20,
1903-1915.
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K.J.Treharne,
D.Cassidy,
C.Goddard,
W.H.Colledge,
A.Cassidy,
and
A.Mehta
(2009).
Epithelial IgG and its relationship to the loss of F508 in the common mutant form of the cystic fibrosis transmembrane conductance regulator.
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FEBS Lett,
583,
2493-2499.
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K.J.Treharne,
Z.Xu,
J.H.Chen,
O.G.Best,
D.M.Cassidy,
D.C.Gruenert,
P.Hegyi,
M.A.Gray,
D.N.Sheppard,
K.Kunzelmann,
and
A.Mehta
(2009).
Inhibition of protein kinase CK2 closes the CFTR Cl channel, but has no effect on the cystic fibrosis mutant deltaF508-CFTR.
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Cell Physiol Biochem,
24,
347-360.
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M.F.Tsai,
H.Shimizu,
Y.Sohma,
M.Li,
and
T.C.Hwang
(2009).
State-dependent modulation of CFTR gating by pyrophosphate.
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J Gen Physiol,
133,
405-419.
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S.Y.Huang,
D.Bolser,
H.Y.Liu,
T.C.Hwang,
and
X.Zou
(2009).
Molecular modeling of the heterodimer of human CFTR's nucleotide-binding domains using a protein-protein docking approach.
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J Mol Graph Model,
27,
822-828.
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U.A.Hellmich,
and
C.Glaubitz
(2009).
NMR and EPR studies of membrane transporters.
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Biol Chem,
390,
815-834.
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A.W.Serohijos,
T.Hegedus,
A.A.Aleksandrov,
L.He,
L.Cui,
N.V.Dokholyan,
and
J.R.Riordan
(2008).
Phenylalanine-508 mediates a cytoplasmic-membrane domain contact in the CFTR 3D structure crucial to assembly and channel function.
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Proc Natl Acad Sci U S A,
105,
3256-3261.
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A.W.Serohijos,
T.Hegedus,
J.R.Riordan,
and
N.V.Dokholyan
(2008).
Diminished self-chaperoning activity of the DeltaF508 mutant of CFTR results in protein misfolding.
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PLoS Comput Biol,
4,
e1000008.
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C.M.Deber,
J.C.Cheung,
and
A.Rath
(2008).
Defining the defect in F508 del CFTR: a soluble problem?
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Chem Biol,
15,
3-4.
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C.S.Rogers,
W.M.Abraham,
K.A.Brogden,
J.F.Engelhardt,
J.T.Fisher,
P.B.McCray,
G.McLennan,
D.K.Meyerholz,
E.Namati,
L.S.Ostedgaard,
R.S.Prather,
J.R.Sabater,
D.A.Stoltz,
J.Zabner,
and
M.J.Welsh
(2008).
The porcine lung as a potential model for cystic fibrosis.
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Am J Physiol Lung Cell Mol Physiol,
295,
L240-L263.
|
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|
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F.Sun,
Z.Mi,
S.B.Condliffe,
C.A.Bertrand,
X.Gong,
X.Lu,
R.Zhang,
J.D.Latoche,
J.M.Pilewski,
P.D.Robbins,
and
R.A.Frizzell
(2008).
Chaperone displacement from mutant cystic fibrosis transmembrane conductance regulator restores its function in human airway epithelia.
|
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FASEB J,
22,
3255-3263.
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J.R.Riordan
(2008).
CFTR function and prospects for therapy.
|
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Annu Rev Biochem,
77,
701-726.
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K.Mio,
T.Ogura,
M.Mio,
H.Shimizu,
T.C.Hwang,
C.Sato,
and
Y.Sohma
(2008).
Three-dimensional reconstruction of human cystic fibrosis transmembrane conductance regulator chloride channel revealed an ellipsoidal structure with orifices beneath the putative transmembrane domain.
|
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J Biol Chem,
283,
30300-30310.
|
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L.He,
A.A.Aleksandrov,
A.W.Serohijos,
T.Hegedus,
L.A.Aleksandrov,
L.Cui,
N.V.Dokholyan,
and
J.R.Riordan
(2008).
Multiple membrane-cytoplasmic domain contacts in the cystic fibrosis transmembrane conductance regulator (CFTR) mediate regulation of channel gating.
|
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J Biol Chem,
283,
26383-26390.
|
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|
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L.S.Pissarra,
C.M.Farinha,
Z.Xu,
A.Schmidt,
P.H.Thibodeau,
Z.Cai,
P.J.Thomas,
D.N.Sheppard,
and
M.D.Amaral
(2008).
Solubilizing mutations used to crystallize one CFTR domain attenuate the trafficking and channel defects caused by the major cystic fibrosis mutation.
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Chem Biol,
15,
62-69.
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P.C.Wen,
and
E.Tajkhorshid
(2008).
Dimer opening of the nucleotide binding domains of ABC transporters after ATP hydrolysis.
|
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Biophys J,
95,
5100-5110.
|
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S.Pagant,
E.Y.Brovman,
J.J.Halliday,
and
E.A.Miller
(2008).
Mapping of interdomain interfaces required for the functional architecture of Yor1p, a eukaryotic ATP-binding cassette (ABC) transporter.
|
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J Biol Chem,
283,
26444-26451.
|
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T.W.Loo,
M.C.Bartlett,
and
D.M.Clarke
(2008).
Processing mutations disrupt interactions between the nucleotide binding and transmembrane domains of P-glycoprotein and the cystic fibrosis transmembrane conductance regulator (CFTR).
|
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J Biol Chem,
283,
28190-28197.
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X.Wang,
A.V.Koulov,
W.A.Kellner,
J.R.Riordan,
and
W.E.Balch
(2008).
Chemical and biological folding contribute to temperature-sensitive DeltaF508 CFTR trafficking.
|
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Traffic,
9,
1878-1893.
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A.A.Aleksandrov,
L.A.Aleksandrov,
and
J.R.Riordan
(2007).
CFTR (ABCC7) is a hydrolyzable-ligand-gated channel.
|
| |
Pflugers Arch,
453,
693-702.
|
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|
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J.L.Jiménez,
B.Hegemann,
J.R.Hutchins,
J.M.Peters,
and
R.Durbin
(2007).
A systematic comparative and structural analysis of protein phosphorylation sites based on the mtcPTM database.
|
| |
Genome Biol,
8,
R90.
|
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|
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J.L.Mendoza,
and
P.J.Thomas
(2007).
Building an understanding of cystic fibrosis on the foundation of ABC transporter structures.
|
| |
J Bioenerg Biomembr,
39,
499-505.
|
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|
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|
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J.M.Baker,
R.P.Hudson,
V.Kanelis,
W.Y.Choy,
P.H.Thibodeau,
P.J.Thomas,
and
J.D.Forman-Kay
(2007).
CFTR regulatory region interacts with NBD1 predominantly via multiple transient helices.
|
| |
Nat Struct Mol Biol,
14,
738-745.
|
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|
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|
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L.S.Ostedgaard,
C.S.Rogers,
Q.Dong,
C.O.Randak,
D.W.Vermeer,
T.Rokhlina,
P.H.Karp,
and
M.J.Welsh
(2007).
Processing and function of CFTR-DeltaF508 are species-dependent.
|
| |
Proc Natl Acad Sci U S A,
104,
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PDB code:
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PDB codes:
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|
The most recent references are shown first.
Citation data come partly from CiteXplore and partly
from an automated harvesting procedure. Note that this is likely to be
only a partial list as not all journals are covered by
either method. However, we are continually building up the citation data
so more and more references will be included with time.
Where a reference describes a PDB structure, the PDB
codes are
shown on the right.
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');
}
}
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