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

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Basic information

Entry
Database: PDB / ID: 5tff
TitleNucleotide-binding domain 1 of the human cystic fibrosis transmembrane conductance regulator (CFTR) with 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 / bicarbonate transport / bicarbonate transmembrane transporter activity / membrane hyperpolarization / vesicle docking involved in exocytosis / chloride channel regulator activity / chloride transmembrane transporter activity / sperm capacitation / cholesterol biosynthetic process / chloride channel activity / RHOQ GTPase cycle / positive regulation of exocytosis / positive regulation of insulin secretion involved in cellular response to glucose stimulus / ATPase-coupled transmembrane transporter activity / chloride channel complex / ABC-type transporter activity / cellular response to cAMP / 14-3-3 protein binding / cellular response to forskolin / chloride transmembrane transport / response to endoplasmic reticulum stress / isomerase activity / PDZ domain binding / establishment of localization in cell / Defective CFTR causes cystic fibrosis / clathrin-coated endocytic vesicle membrane / Late endosomal microautophagy / recycling endosome / ABC-family proteins mediated transport / transmembrane transport / recycling endosome membrane / Chaperone Mediated Autophagy / Aggrephagy / 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 / protein-containing complex / ATP hydrolysis activity / ATP binding / nucleus / membrane / 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
URIDINE 5'-TRIPHOSPHATE / Cystic fibrosis transmembrane conductance regulator
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.891 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

Downloads & links

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Assembly

Deposited unit
A: Cystic fibrosis transmembrane conductance regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,0343
Polymers25,5251
Non-polymers5082
Water3,531196
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)40.183, 40.183, 141.794
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-UTP / URIDINE 5'-TRIPHOSPHATE


Mass: 484.141 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H15N2O15P3 / Comment: UTP*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 196 / 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: 48.36 %
Crystal growTemperature: 279 K / Method: microbatch / pH: 7.5
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: 1.89→50 Å / Num. obs: 17909 / % possible obs: 100 % / Redundancy: 7.6 % / Net I/σ(I): 44.4

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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: 1.891→40.183 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.42 / Phase error: 17.33
RfactorNum. reflection% reflection
Rfree0.1897 1804 10.07 %
Rwork0.1595 --
obs0.1625 17907 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.891→40.183 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1652 0 30 196 1878
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071710
X-RAY DIFFRACTIONf_angle_d0.9042310
X-RAY DIFFRACTIONf_dihedral_angle_d19.5131009
X-RAY DIFFRACTIONf_chiral_restr0.056262
X-RAY DIFFRACTIONf_plane_restr0.004286
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8911-1.94220.19791390.16261219X-RAY DIFFRACTION100
1.9422-1.99940.19511370.15421266X-RAY DIFFRACTION100
1.9994-2.06390.19051350.15351204X-RAY DIFFRACTION100
2.0639-2.13770.19211410.14311269X-RAY DIFFRACTION100
2.1377-2.22320.17641410.14491219X-RAY DIFFRACTION100
2.2232-2.32440.19041360.14971229X-RAY DIFFRACTION100
2.3244-2.44690.1841410.16281243X-RAY DIFFRACTION100
2.4469-2.60020.21291360.16081233X-RAY DIFFRACTION100
2.6002-2.80090.17341400.16411239X-RAY DIFFRACTION100
2.8009-3.08270.19181370.17511258X-RAY DIFFRACTION100
3.0827-3.52860.19261360.16031234X-RAY DIFFRACTION100
3.5286-4.44470.16471430.14841245X-RAY DIFFRACTION100
4.4447-40.19210.21921420.17471245X-RAY DIFFRACTION100

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