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- PDB-5tfg: Nucleotide-binding domain 1 of the human cystic fibrosis transmem... -

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Basic information

Entry
Database: PDB / ID: 5tfg
TitleNucleotide-binding domain 1 of the human cystic fibrosis transmembrane conductance regulator (CFTR) with 5-methyl-UTP
ComponentsCystic fibrosis transmembrane conductance regulator
KeywordsHYDROLASE / hNBD1 / CFTR / ABC transport / ATP
Function / homology
Function and homology information


positive regulation of voltage-gated chloride channel activity / positive regulation of cyclic nucleotide-gated ion channel activity / Sec61 translocon complex binding / channel-conductance-controlling ATPase / intracellularly ATP-gated chloride channel activity / positive regulation of enamel mineralization / transepithelial water transport / RHO GTPases regulate CFTR trafficking / intracellular pH elevation / amelogenesis ...positive regulation of voltage-gated chloride channel activity / positive regulation of cyclic nucleotide-gated ion channel activity / Sec61 translocon complex binding / channel-conductance-controlling ATPase / intracellularly ATP-gated chloride channel activity / positive regulation of enamel mineralization / transepithelial water transport / RHO GTPases regulate CFTR trafficking / intracellular pH elevation / amelogenesis / chloride channel inhibitor activity / ATPase-coupled inorganic anion transmembrane transporter activity / Golgi-associated vesicle membrane / multicellular organismal-level water homeostasis / cholesterol transport / membrane hyperpolarization / vesicle docking involved in exocytosis / bicarbonate transport / bicarbonate transmembrane transporter activity / chloride channel regulator activity / chloride transmembrane transporter activity / sperm capacitation / chloride channel activity / cholesterol biosynthetic process / RHOQ GTPase cycle / positive regulation of insulin secretion involved in cellular response to glucose stimulus / positive regulation of exocytosis / chloride channel complex / ATPase-coupled transmembrane transporter activity / ABC-type transporter activity / cellular response to forskolin / cellular response to cAMP / chloride transmembrane transport / response to endoplasmic reticulum stress / isomerase activity / establishment of localization in cell / PDZ domain binding / Defective CFTR causes cystic fibrosis / Late endosomal microautophagy / clathrin-coated endocytic vesicle membrane / ABC-family proteins mediated transport / transmembrane transport / recycling endosome / Aggrephagy / Chaperone Mediated Autophagy / recycling endosome membrane / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / protein-folding chaperone binding / early endosome membrane / early endosome / endosome membrane / Ub-specific processing proteases / apical plasma membrane / lysosomal membrane / endoplasmic reticulum membrane / enzyme binding / cell surface / ATP hydrolysis activity / protein-containing complex / ATP binding / membrane / nucleus / plasma membrane / cytosol / cytoplasm
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 ...: / 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 / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
5-Methyluridine triphosphate / Cystic fibrosis transmembrane conductance regulator
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.91 Å
AuthorsWang, C. / Aleksandrov, A.A. / Yang, Z. / Forouhar, F. / Proctor, E. / Kota, P. / An, J. / Kaplan, A. / Khazanov, N. / Boel, G. ...Wang, C. / Aleksandrov, A.A. / Yang, Z. / Forouhar, F. / Proctor, E. / Kota, P. / An, J. / Kaplan, A. / Khazanov, N. / Boel, G. / Stockwell, B.R. / Senderowitz, H. / Dokholyan, N.V. / Riordan, J.R. / Brouillette, C.G. / Hunt, J.F.
Funding support United States, 1items
OrganizationGrant numberCountry
Cystic Fibrosis FoundationHunt13XX0 United States
CitationJournal: To Be Published
Title: Thermodynamic correction of F508del-CFTR by ligand binding to a remote site in the mutated domain
Authors: Wang, C. / Aleksandrov, A.A. / Yang, Z. / Forouhar, F. / Proctor, E. / Kota, P. / An, J. / Kaplan, A. / Khazanov, N. / Boel, G. / Stockwell, B.R. / Senderowitz, H. / Dokholyan, N.V. / ...Authors: Wang, C. / Aleksandrov, A.A. / Yang, Z. / Forouhar, F. / Proctor, E. / Kota, P. / An, J. / Kaplan, A. / Khazanov, N. / Boel, G. / Stockwell, B.R. / Senderowitz, H. / Dokholyan, N.V. / Riordan, J.R. / Brouillette, C.G. / Hunt, J.F.
History
DepositionSep 25, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 9, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cystic fibrosis transmembrane conductance regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,0483
Polymers25,5251
Non-polymers5222
Water3,423190
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)40.147, 40.147, 141.787
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

#1: Protein Cystic fibrosis transmembrane conductance regulator / CFTR / ATP-binding cassette sub-family C member 7 / Channel conductance-controlling ATPase / cAMP- ...CFTR / ATP-binding cassette sub-family C member 7 / Channel conductance-controlling ATPase / cAMP-dependent chloride channel


Mass: 25525.408 Da / Num. of mol.: 1
Fragment: Nucleotide-binding domain 1 (UNP residues 387-646)
Mutation: V470M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CFTR, ABCC7
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P13569, EC: 3.6.3.49
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-M5T / 5-Methyluridine triphosphate


Mass: 498.168 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N2O15P3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 190 / Source method: isolated from a natural source / Formula: H2O

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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: 2.38 Å3/Da / Density % sol: 48.26 %
Crystal growTemperature: 279 K / Method: microbatch
Details: Protein buffer: 150 mM NaCl, 30% (v/v) glycerol, 1 mM TCEP, and 20 mM Na-HEPES, pH 7.5; Precipitant buffer: 40% (v/v) PEG 400, 100 mM NH4Cl, and 100 mM MES, pH 6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 1.18076 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 28, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.18076 Å / Relative weight: 1
ReflectionResolution: 1.91→50 Å / Num. obs: 16965 / % possible obs: 97.7 % / Redundancy: 7.8 % / Net I/σ(I): 60.5

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2pze

2pze


Resolution: 1.91→40.147 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 18.14
RfactorNum. reflection% reflection
Rfree0.1836 1714 10.1 %
Rwork0.1563 --
obs0.1591 16962 97.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.91→40.147 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1652 0 31 190 1873
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091717
X-RAY DIFFRACTIONf_angle_d1.1122321
X-RAY DIFFRACTIONf_dihedral_angle_d19.7511016
X-RAY DIFFRACTIONf_chiral_restr0.053263
X-RAY DIFFRACTIONf_plane_restr0.004287
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9101-1.96630.21971360.16491215X-RAY DIFFRACTION96
1.9663-2.02970.19921420.151253X-RAY DIFFRACTION97
2.0297-2.10230.20531370.14721274X-RAY DIFFRACTION97
2.1023-2.18640.23241450.15021255X-RAY DIFFRACTION97
2.1864-2.28590.18491320.1491249X-RAY DIFFRACTION98
2.2859-2.40640.18291480.15241276X-RAY DIFFRACTION98
2.4064-2.55720.18831400.1511281X-RAY DIFFRACTION98
2.5572-2.75460.16991400.16051273X-RAY DIFFRACTION99
2.7546-3.03170.21621540.16121278X-RAY DIFFRACTION99
3.0317-3.47020.17261420.15661293X-RAY DIFFRACTION99
3.4702-4.37120.16611500.14151301X-RAY DIFFRACTION99
4.3712-40.15590.16521480.17741300X-RAY DIFFRACTION99

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