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- PDB-5tf7: Nucleotide-binding domain 1 of the human cystic fibrosis transmem... -

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Basic information

Entry
Database: PDB / ID: 5tf7
TitleNucleotide-binding domain 1 of the human cystic fibrosis transmembrane conductance regulator (CFTR) with ATP
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 / bicarbonate transport / vesicle docking involved in exocytosis / 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 cAMP / chloride transmembrane transport / cellular response to forskolin / 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 / recycling endosome / transmembrane transport / 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
ADENOSINE-5'-TRIPHOSPHATE / Cystic fibrosis transmembrane conductance regulator
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.931 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 24, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 9, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2023Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_audit_support / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization

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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)26,0573
Polymers25,5251
Non-polymers5312
Water3,027168
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)40.288, 40.288, 141.165
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-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 168 / 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: 48.3 %
Crystal growTemperature: 279 K / Method: microbatch / pH: 7.5
Details: 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 27, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.18076 Å / Relative weight: 1
ReflectionResolution: 1.93→50 Å / Num. obs: 123451 / % possible obs: 99.4 % / Redundancy: 7.4 % / Net I/σ(I): 47.6

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Processing

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

2pze


Resolution: 1.931→40.288 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.42 / Phase error: 19.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1995 1681 10.05 %
Rwork0.1569 --
obs0.1612 16727 99.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.931→40.288 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1670 0 32 168 1870
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071731
X-RAY DIFFRACTIONf_angle_d0.8682337
X-RAY DIFFRACTIONf_dihedral_angle_d18.7251022
X-RAY DIFFRACTIONf_chiral_restr0.052264
X-RAY DIFFRACTIONf_plane_restr0.004288
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9305-1.98730.20971370.14911217X-RAY DIFFRACTION98
1.9873-2.05150.20711310.14651242X-RAY DIFFRACTION98
2.0515-2.12480.21751370.14861276X-RAY DIFFRACTION99
2.1248-2.20990.191430.14841238X-RAY DIFFRACTION99
2.2099-2.31040.16741380.14571248X-RAY DIFFRACTION99
2.3104-2.43220.21851410.1581244X-RAY DIFFRACTION100
2.4322-2.58460.19931460.16251256X-RAY DIFFRACTION99
2.5846-2.78410.21851360.1641240X-RAY DIFFRACTION100
2.7841-3.06420.23141440.17331284X-RAY DIFFRACTION100
3.0642-3.50740.18781380.16021250X-RAY DIFFRACTION100
3.5074-4.4180.1821450.14351281X-RAY DIFFRACTION100
4.418-40.29680.19911450.16681270X-RAY DIFFRACTION100

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