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- PDB-1xfa: Structure of NBD1 from murine CFTR- F508R mutant -

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Basic information

Entry
Database: PDB / ID: 1xfa
TitleStructure of NBD1 from murine CFTR- F508R mutant
ComponentsCystic fibrosis transmembrane conductance regulator
KeywordsTRANSPORT PROTEIN / Cystic Fibrosis / ABC transporters / ATP / nucleotide-binding domain
Function / homology
Function and homology information


RHO GTPases regulate CFTR trafficking / RHOQ GTPase cycle / positive regulation of mast cell activation / transepithelial chloride transport / positive regulation of establishment of Sertoli cell barrier / Aggrephagy / positive regulation of cyclic nucleotide-gated ion channel activity / Sec61 translocon complex binding / channel-conductance-controlling ATPase / intracellularly ATP-gated chloride channel activity ...RHO GTPases regulate CFTR trafficking / RHOQ GTPase cycle / positive regulation of mast cell activation / transepithelial chloride transport / positive regulation of establishment of Sertoli cell barrier / Aggrephagy / positive regulation of cyclic nucleotide-gated ion channel activity / Sec61 translocon complex binding / channel-conductance-controlling ATPase / intracellularly ATP-gated chloride channel activity / water transport / positive regulation of enamel mineralization / transepithelial water transport / negative regulation of vascular associated smooth muscle cell apoptotic process / intracellular pH elevation / enamel mineralization / negative regulation of type B pancreatic cell development / amelogenesis / chloride channel inhibitor activity / Cargo recognition for clathrin-mediated endocytosis / ABC-family proteins mediated transport / Clathrin-mediated endocytosis / multicellular organismal-level water homeostasis / vesicle docking involved in exocytosis / Ub-specific processing proteases / membrane hyperpolarization / cholesterol transport / bicarbonate transport / bicarbonate transmembrane transporter activity / chloride transport / chloride transmembrane transporter activity / sperm capacitation / chloride channel activity / cholesterol biosynthetic process / positive regulation of exocytosis / positive regulation of insulin secretion involved in cellular response to glucose stimulus / microvillus / chloride channel complex / ATPase-coupled transmembrane transporter activity / sodium ion transmembrane transport / ABC-type transporter activity / cellular response to cAMP / cellular response to forskolin / isomerase activity / chloride transmembrane transport / response to endoplasmic reticulum stress / establishment of localization in cell / PDZ domain binding / lung development / recycling endosome membrane / vasodilation / protein-folding chaperone binding / early endosome membrane / basolateral plasma membrane / early endosome / response to xenobiotic stimulus / apical plasma membrane / neuronal cell body / dendrite / endoplasmic reticulum membrane / enzyme binding / cell surface / ATP hydrolysis activity / ATP binding / membrane / nucleus / plasma membrane / cytosol
Similarity search - Function
: / CFTR regulator domain / Cystic fibrosis TM conductance regulator (CFTR), regulator domain / Cystic fibrosis transmembrane conductance regulator / ABC transporter transmembrane region / ABC transporter type 1, transmembrane domain / ABC transporter integral membrane type-1 fused domain profile. / ABC transporter type 1, transmembrane domain superfamily / ABC transporter-like, conserved site / ABC transporters family signature. ...: / CFTR regulator domain / Cystic fibrosis TM conductance regulator (CFTR), regulator domain / Cystic fibrosis transmembrane conductance regulator / ABC transporter transmembrane region / ABC transporter type 1, transmembrane domain / ABC transporter integral membrane type-1 fused domain profile. / ABC transporter type 1, transmembrane domain superfamily / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETIC ACID / ADENOSINE-5'-TRIPHOSPHATE / Cystic fibrosis transmembrane conductance regulator
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsThibodeau, P.H. / Brautigam, C.A. / Machius, M. / Thomas, P.J.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2005
Title: Side chain and backbone contributions of Phe508 to CFTR folding.
Authors: Thibodeau, P.H. / Brautigam, C.A. / Machius, M. / Thomas, P.J.
History
DepositionSep 14, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 28, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cystic fibrosis transmembrane conductance regulator
B: Cystic fibrosis transmembrane conductance regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,93212
Polymers63,5582
Non-polymers1,37410
Water0
1
A: Cystic fibrosis transmembrane conductance regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,5027
Polymers31,7791
Non-polymers7226
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cystic fibrosis transmembrane conductance regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,4315
Polymers31,7791
Non-polymers6524
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)139.994, 139.994, 278.721
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122

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Components

#1: Protein Cystic fibrosis transmembrane conductance regulator / / CFTR / cAMP-dependent chloride channel


Mass: 31779.041 Da / Num. of mol.: 2 / Fragment: NBD1 / Mutation: F508R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cftr, Abcc7 / Plasmid: pSmt3-nbd1-f508r / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Codon Plus / References: UniProt: P26361
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#5: Chemical
ChemComp-ACY / ACETIC ACID / Acetic acid


Mass: 60.052 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H4O2

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 6.5 Å3/Da / Density % sol: 81 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Sodium acetate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.98 Å
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Jun 4, 2004
RadiationMonochromator: Double-crystal monochromator, Si-111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3.1→44.3 Å / Num. all: 25581 / Num. obs: 25581 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 11.9 % / Rsym value: 0.071 / Net I/σ(I): 34.8
Reflection shellResolution: 3.1→3.15 Å / Redundancy: 10.7 % / Mean I/σ(I) obs: 2.5 / Num. unique all: 1260 / Rsym value: 0.987 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
CNS1.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ROX monomer, stripped of heterogens

1rox
PDB Unreleased entry


Resolution: 3.1→44.27 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 155216.5 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.261 1356 5.6 %RANDOM
Rwork0.249 ---
all0.25 24188 --
obs0.25 24188 94.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 21.9149 Å2 / ksol: 0.325347 e/Å3
Displacement parametersBiso mean: 86.3 Å2
Baniso -1Baniso -2Baniso -3
1-6.2 Å20 Å20 Å2
2--6.2 Å20 Å2
3----12.41 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.48 Å0.43 Å
Luzzati d res low-5 Å
Luzzati sigma a0.68 Å0.65 Å
Refinement stepCycle: LAST / Resolution: 3.1→44.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4166 0 66 16 4248
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d22.7
X-RAY DIFFRACTIONc_improper_angle_d0.81
X-RAY DIFFRACTIONc_mcbond_it1.31.5
X-RAY DIFFRACTIONc_mcangle_it2.312
X-RAY DIFFRACTIONc_scbond_it1.832
X-RAY DIFFRACTIONc_scangle_it3.072.5
LS refinement shellResolution: 3.1→3.29 Å / Rfactor Rfree error: 0.03 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.432 213 5.8 %
Rwork0.405 3447 -
obs-3660 87.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAM
X-RAY DIFFRACTION3ATP_DRG.PARAM
X-RAY DIFFRACTION4ACY_DRG.PARAM

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