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PDBsum entry 1xmi

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protein ligands metals Protein-protein interface(s) links
Membrane protein, hydrolase PDB id
1xmi

 

 

 

 

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Contents
Protein chain
267 a.a. *
Ligands
ATP ×5
Metals
_MG ×5
Waters ×704
* Residue conservation analysis
PDB id:
1xmi
Name: Membrane protein, hydrolase
Title: Crystal structure of human f508a nbd1 domain with atp
Structure: 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
Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: cftr. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Pentamer (from PQS)
Resolution:
2.25Å     R-factor:   0.232     R-free:   0.265
Authors: 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
Key ref:
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: 15528182 DOI: 10.1074/jbc.M410968200
Date:
02-Oct-04     Release date:   09-Nov-04    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P13569  (CFTR_HUMAN) -  Cystic fibrosis transmembrane conductance regulator from Homo sapiens
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
1480 a.a.
267 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 5 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: E.C.5.6.1.6  - channel-conductance-controlling ATPase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: ATP + H2O + closed Cl- channel = ADP + phosphate + open Cl- channel
ATP
Bound ligand (Het Group name = ATP)
corresponds exactly
+ H2O
+ closed Cl(-) channel
= ADP
+ phosphate
+ open Cl(-) channel
Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 

 
    reference    
 
 
DOI no: 10.1074/jbc.M410968200 J Biol Chem 280:1346-1353 (2005)
PubMed id: 15528182  
 
 
Impact of the deltaF508 mutation in first nucleotide-binding domain of human cystic fibrosis transmembrane conductance regulator on domain folding and structure.
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.
 
  ABSTRACT  
 
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.
 
  Selected figure(s)  
 
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).
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).
 
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2005, 280, 1346-1353) copyright 2005.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21419343 A.Khushoo, Z.Yang, A.E.Johnson, and W.R.Skach (2011).
Ligand-driven vectorial folding of ribosome-bound human CFTR NBD1.
  Mol Cell, 41, 682-692.  
21275046 E.Noy, and H.Senderowitz (2011).
Combating Cystic Fibrosis: In Search for CF Transmembrane Conductance Regulator (CFTR) Modulators.
  ChemMedChem, 6, 243-251.  
20687163 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.
  Protein Sci, 19, 1932-1947.  
20032308 G.Roy, E.M.Chalfin, A.Saxena, and X.Wang (2010).
Interplay between ER exit code and domain conformation in CFTR misprocessing and rescue.
  Mol Biol Cell, 21, 597-609.  
21152102 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.
  PLoS One, 5, e15458.  
20687133 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.
  Protein Sci, 19, 1917-1931.  
20653506 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.
  Expert Rev Proteomics, 7, 495-506.  
19903491 J.L.Kreindler (2010).
Cystic fibrosis: exploiting its genetic basis in the hunt for new therapies.
  Pharmacol Ther, 125, 219-229.  
  20421370 M.F.Tsai, M.Li, and T.C.Hwang (2010).
Stable ATP binding mediated by a partial NBD dimer of the CFTR chloride channel.
  J Gen Physiol, 135, 399-414.  
20823549 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.
  Acta Crystallogr D Biol Crystallogr, 66, 979-987.
PDB codes: 3nh6 3nh9 3nha 3nhb
20976528 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.
  J Comput Aided Mol Des, 24, 971-991.  
20150177 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.
  Protein Eng Des Sel, 23, 375-384.
PDB codes: 2pze 2pzf 2pzg
19802819 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.
  Biopolymers, 93, 237-251.  
20590134 T.W.Loo, M.C.Bartlett, and D.M.Clarke (2010).
The V510D suppressor mutation stabilizes DeltaF508-CFTR at the cell surface.
  Biochemistry, 49, 6352-6357.  
19927121 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.
  EMBO J, 29, 263-277.  
19707853 J.P.Mornon, P.Lehn, and I.Callebaut (2009).
Molecular models of the open and closed states of the whole human CFTR protein.
  Cell Mol Life Sci, 66, 3469-3486.  
19176754 K.Du, and G.L.Lukacs (2009).
Cooperative assembly and misfolding of CFTR domains in vivo.
  Mol Biol Cell, 20, 1903-1915.  
19596328 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.
  FEBS Lett, 583, 2493-2499.  
19910675 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.
  Cell Physiol Biochem, 24, 347-360.  
  19332621 M.F.Tsai, H.Shimizu, Y.Sohma, M.Li, and T.C.Hwang (2009).
State-dependent modulation of CFTR gating by pyrophosphate.
  J Gen Physiol, 133, 405-419.  
19167254 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.
  J Mol Graph Model, 27, 822-828.  
19453273 U.A.Hellmich, and C.Glaubitz (2009).
NMR and EPR studies of membrane transporters.
  Biol Chem, 390, 815-834.  
18305154 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.
  Proc Natl Acad Sci U S A, 105, 3256-3261.  
18463704 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.
  PLoS Comput Biol, 4, e1000008.  
18215767 C.M.Deber, J.C.Cheung, and A.Rath (2008).
Defining the defect in F508 del CFTR: a soluble problem?
  Chem Biol, 15, 3-4.  
18487356 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.
  Am J Physiol Lung Cell Mol Physiol, 295, L240-L263.  
18556464 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.
  FASEB J, 22, 3255-3263.  
18304008 J.R.Riordan (2008).
CFTR function and prospects for therapy.
  Annu Rev Biochem, 77, 701-726.  
18723516 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.
  J Biol Chem, 283, 30300-30310.  
18658148 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.
  J Biol Chem, 283, 26383-26390.  
18215773 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.
  Chem Biol, 15, 62-69.  
18790847 P.C.Wen, and E.Tajkhorshid (2008).
Dimer opening of the nucleotide binding domains of ABC transporters after ATP hydrolysis.
  Biophys J, 95, 5100-5110.  
18644782 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.
  J Biol Chem, 283, 26444-26451.  
18708637 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).
  J Biol Chem, 283, 28190-28197.  
18764821 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.
  Traffic, 9, 1878-1893.  
17021796 A.A.Aleksandrov, L.A.Aleksandrov, and J.R.Riordan (2007).
CFTR (ABCC7) is a hydrolyzable-ligand-gated channel.
  Pflugers Arch, 453, 693-702.  
17521420 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.  
18080175 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.  
17660831 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.  
17873061 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, 15370-15375.  
17615300 S.Pagant, L.Kung, M.Dorrington, M.C.Lee, and E.A.Miller (2007).
Inhibiting endoplasmic reticulum (ER)-associated degradation of misfolded Yor1p does not permit ER export despite the presence of a diacidic sorting signal.
  Mol Biol Cell, 18, 3398-3413.  
16541253 C.Oswald, I.B.Holland, and L.Schmitt (2006).
The motor domains of ABC-transporters. What can structures tell us?
  Naunyn Schmiedebergs Arch Pharmacol, 372, 385-399.  
16554808 D.C.Gadsby, P.Vergani, and L.Csanády (2006).
The ABC protein turned chloride channel whose failure causes cystic fibrosis.
  Nature, 440, 477-483.  
  16632633 F.J.Accurso (2006).
Update in cystic fibrosis 2005.
  Am J Respir Crit Care Med, 173, 944-947.  
16484308 L.Cui, L.Aleksandrov, Y.X.Hou, M.Gentzsch, J.H.Chen, J.R.Riordan, and A.A.Aleksandrov (2006).
The role of cystic fibrosis transmembrane conductance regulator phenylalanine 508 side chain in ion channel gating.
  J Physiol, 572, 347-358.  
17036051 M.Mense, P.Vergani, D.M.White, G.Altberg, A.C.Nairn, and D.C.Gadsby (2006).
In vivo phosphorylation of CFTR promotes formation of a nucleotide-binding domain heterodimer.
  EMBO J, 25, 4728-4739.  
17098864 M.Roxo-Rosa, Z.Xu, A.Schmidt, M.Neto, Z.Cai, C.M.Soares, D.N.Sheppard, and M.D.Amaral (2006).
Revertant mutants G550E and 4RK rescue cystic fibrosis mutants in the first nucleotide-binding domain of CFTR by different mechanisms.
  Proc Natl Acad Sci U S A, 103, 17891-17896.  
16943773 R.J.Dawson, and K.P.Locher (2006).
Structure of a bacterial multidrug ABC transporter.
  Nature, 443, 180-185.
PDB code: 2hyd
  16966475 Z.Zhou, X.Wang, H.Y.Liu, X.Zou, M.Li, and T.C.Hwang (2006).
The two ATP binding sites of cystic fibrosis transmembrane conductance regulator (CFTR) play distinct roles in gating kinetics and energetics.
  J Gen Physiol, 128, 413-422.  
15689966 D.M.Cyr (2005).
Arrest of CFTRDeltaF508 folding.
  Nat Struct Mol Biol, 12, 2-3.  
16691486 J.E.Moody, and P.J.Thomas (2005).
Nucleotide binding domain interactions during the mechanochemical reaction cycle of ATP-binding cassette transporters.
  J Bioenerg Biomembr, 37, 475-479.  
15619635 K.Du, M.Sharma, and G.L.Lukacs (2005).
The DeltaF508 cystic fibrosis mutation impairs domain-domain interactions and arrests post-translational folding of CFTR.
  Nat Struct Mol Biol, 12, 17-25.  
15619636 P.H.Thibodeau, C.A.Brautigam, M.Machius, and P.J.Thomas (2005).
Side chain and backbone contributions of Phe508 to CFTR folding.
  Nat Struct Mol Biol, 12, 10-16.
PDB codes: 1xf9 1xfa
16246032 P.Vergani, C.Basso, M.Mense, A.C.Nairn, and D.C.Gadsby (2005).
Control of the CFTR channel's gates.
  Biochem Soc Trans, 33, 1003-1007.  
16691490 T.W.Loo, M.C.Bartlett, and D.M.Clarke (2005).
Rescue of folding defects in ABC transporters using pharmacological chaperones.
  J Bioenerg Biomembr, 37, 501-507.  
16223764 Z.Zhou, X.Wang, M.Li, Y.Sohma, X.Zou, and T.C.Hwang (2005).
High affinity ATP/ADP analogues as new tools for studying CFTR gating.
  J Physiol, 569, 447-457.  
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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