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- PDB-6wbs: Human CFTR first nucleotide binding domain with dF508/V510D -

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Basic information

Entry
Database: PDB / ID: 6wbs
TitleHuman CFTR first nucleotide binding domain with dF508/V510D
ComponentsCystic fibrosis transmembrane conductance regulator
KeywordsHYDROLASE / Ion Channel / ATP Binding
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 / membrane hyperpolarization / cholesterol transport / bicarbonate transport / bicarbonate transmembrane transporter activity / vesicle docking involved in exocytosis / chloride channel regulator activity / chloride transmembrane transporter activity / sperm capacitation / chloride channel activity / RHOQ GTPase cycle / cholesterol biosynthetic process / positive regulation of exocytosis / positive regulation of insulin secretion involved in cellular response to glucose stimulus / chloride channel complex / ATPase-coupled transmembrane transporter activity / ABC-type transporter activity / cellular response to cAMP / cellular response to forskolin / chloride transmembrane transport / isomerase activity / response to endoplasmic reticulum stress / 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 / early endosome membrane / protein-folding chaperone binding / 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 / cytoplasm / 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. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
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: 1.857 Å
AuthorsSimon, K.S. / Kothe, M. / Hilbert, B. / Batchelor, J.D. / Hurlbut, G.D.
Funding support United States, 1items
OrganizationGrant numberCountry
Cystic Fibrosis Foundation United States
CitationJournal: To Be Published
Title: Determining the Molecular Mechanism of Suppressor Mutation V510D and the Contribution of Helical Unraveling to the dF508-CFTR Defect
Authors: Simon, K.S. / Nagarajan, K. / Mechin, I. / Duffy, C. / Manavalan, P. / Altmann, S. / Majewski, A. / Foley, J. / Kaczmarak, J.S. / Bercury, S. / Maderia, M. / Hilbert, B. / Batchelor, J.D. / ...Authors: Simon, K.S. / Nagarajan, K. / Mechin, I. / Duffy, C. / Manavalan, P. / Altmann, S. / Majewski, A. / Foley, J. / Kaczmarak, J.S. / Bercury, S. / Maderia, M. / Hilbert, B. / Batchelor, J.D. / Ziegler, R. / Bajko, J. / Kothe, M. / Scheule, R. / Nair, A. / Hurlbut, G.D.
History
DepositionMar 27, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 7, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 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
B: Cystic fibrosis transmembrane conductance regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,3876
Polymers50,3242
Non-polymers1,0634
Water7,782432
1
A: Cystic fibrosis transmembrane conductance regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,6933
Polymers25,1621
Non-polymers5312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cystic fibrosis transmembrane conductance regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,6933
Polymers25,1621
Non-polymers5312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.396, 81.660, 100.404
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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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: 25161.887 Da / Num. of mol.: 2 / Mutation: deltaF508, V510D, delta405-436
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CFTR, ABCC7 / Variant: deltaRI / Cell line (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 / Variant (production host): DE3(Codon+)
References: UniProt: P13569, channel-conductance-controlling ATPase
#2: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 432 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.59 Å3/Da / Density % sol: 52.6 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: CFTR NBD1 V510D in buffer A was crystallized by mixing equal amounts of protein at 6 mg/mL with 0.1 M Tris pH 7.6, 28% (w/v) polyethylene glycol 10,000. Crystallization was induced by streak- ...Details: CFTR NBD1 V510D in buffer A was crystallized by mixing equal amounts of protein at 6 mg/mL with 0.1 M Tris pH 7.6, 28% (w/v) polyethylene glycol 10,000. Crystallization was induced by streak-seeding using crystals grown in 0.1 M HEPES, pH 7.5, 25% (w/v) polyethylene glycol 550 monomethylether, and plates incubated at 4C. Crystals grew over several days and were frozen by quick dip in reservoir solution supplemented with 25% (w/v) ethylene glycol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.9786 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 18, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 1.857→50 Å / Num. obs: 43865 / % possible obs: 100 % / Redundancy: 6 % / Biso Wilson estimate: 20.97 Å2 / Rmerge(I) obs: 0.124 / Rpim(I) all: 0.055 / Rrim(I) all: 0.127 / Χ2: 1.062 / Net I/σ(I): 7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allΧ2% possible allRrim(I) all
1.86-1.935.70.91642840.7410.411.069100
1.93-260.61443520.8510.271.0861000.673
2-2.096.10.44543130.930.1941.0861000.486
2.09-2.216.20.33343250.9440.1451.0851000.364
2.21-2.346.20.24443560.970.1071.0681000.267
2.34-2.526.20.19143650.980.0831.051000.208
2.52-2.786.20.13943640.9890.0611.0331000.152
2.78-3.186.10.11343990.9910.051.0741000.123
3.18-4.015.90.07744540.9950.0351.0451000.085
4.01-505.60.0546530.9970.0231.0299.90.055

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.13_2998refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2BBS

2bbs


Resolution: 1.857→42.767 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.51
RfactorNum. reflection% reflection
Rfree0.2127 2116 4.83 %
Rwork0.1697 --
obs0.1718 43792 99.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 129.64 Å2 / Biso mean: 31.9829 Å2 / Biso min: 8.56 Å2
Refinement stepCycle: final / Resolution: 1.857→42.767 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3434 0 88 432 3954
Biso mean--28.62 36.74 -
Num. residues----440
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013621
X-RAY DIFFRACTIONf_angle_d1.1844904
X-RAY DIFFRACTIONf_dihedral_angle_d21.1012194
X-RAY DIFFRACTIONf_chiral_restr0.061553
X-RAY DIFFRACTIONf_plane_restr0.006612
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.857-1.90.34781290.2803255192
1.9-1.94750.29531390.23322740100
1.9475-2.00020.25921400.21112747100
2.0002-2.0590.22281410.19582752100
2.059-2.12550.25871390.18442758100
2.1255-2.20140.20731400.18262759100
2.2014-2.28960.21241420.16922774100
2.2896-2.39380.18431410.15822789100
2.3938-2.520.21961400.16542769100
2.52-2.67780.20631410.16512770100
2.6778-2.88450.23761420.16662796100
2.8845-3.17470.20641430.16622797100
3.1747-3.63390.21481430.15772835100
3.6339-4.57750.16031460.13592852100
4.5775-42.7670.21271500.17522987100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.7290.13771.30951.40010.21051.4642-0.0716-0.13380.06940.1265-0.0426-0.20970.00440.02780.11840.14080.0180.00480.13360.00230.187321.6324-12.66945.2567
21.1863-0.05110.67861.3502-0.9111.5773-0.0573-0.11520.09620.10010.0448-0.0876-0.1524-0.15910.0120.10730.01540.00240.0867-0.0280.110516.1859-8.72025.6533
31.2209-0.68740.48130.7484-0.08750.2822-0.0745-0.04840.0830.1243-0.0769-0.1009-0.26730.00330.12290.23910.05010.01970.15190.0210.18920.5929-0.2902-7.3575
41.4873-1.5426-0.02691.8290.34860.8456-0.02380.51320.02-0.3725-0.07330.20610.0501-0.05510.05420.23640.0008-0.03460.20430.01420.1681-1.1782-3.0697-18.9701
52.26960.19390.97871.5712-0.24561.5065-0.03240.0798-0.08280.00180.03510.14090.0709-0.08670.04290.1311-0.00310.04240.105-0.01170.1032.7659-9.5922-9.4836
61.724-0.590.98951.6481-0.31111.9490.16190.3138-0.1872-0.2301-0.04570.02190.25550.2515-0.04980.14450.02960.02510.1445-0.02750.127518.6846-19.5853-6.5743
71.6795-0.9276-0.24321.93910.06161.48170.0495-0.1914-0.0890.2622-0.0261-0.15410.22810.0084-0.01640.24280.0012-0.07040.16130.02440.19326.42558.519414.9741
81.2213-0.01730.69840.92440.51531.56610.0711-0.0239-0.12810.18660.0127-0.10070.22370.0308-0.09730.13650.0026-0.02470.0990.00450.142325.27810.5137.5936
92.3990.5681-0.3731.904-0.02071.7489-0.04710.4550.0218-0.2950.1115-0.0381-0.0043-0.0059-0.06770.136-0.01860.00150.2315-0.00790.123625.923820.2061-15.4161
100.70360.4192-0.17322.6429-0.72131.19380.04620.10570.0748-0.0054-0.03050.0359-0.03530.0391-0.03150.1241-0.006-0.00090.1475-0.00160.139321.007922.9403-2.1324
111.9195-0.1034-0.00861.88310.2231.95050.0634-0.20760.25240.36950.0071-0.0315-0.15590.0106-0.05380.2212-0.03620.00710.1475-0.02690.170322.692625.010714.9288
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 420 through 458 )A420 - 458
2X-RAY DIFFRACTION2chain 'A' and (resid 459 through 491 )A459 - 491
3X-RAY DIFFRACTION3chain 'A' and (resid 492 through 513 )A492 - 513
4X-RAY DIFFRACTION4chain 'A' and (resid 514 through 538 )A514 - 538
5X-RAY DIFFRACTION5chain 'A' and (resid 539 through 589 )A539 - 589
6X-RAY DIFFRACTION6chain 'A' and (resid 590 through 635 )A590 - 635
7X-RAY DIFFRACTION7chain 'B' and (resid 421 through 449 )B421 - 449
8X-RAY DIFFRACTION8chain 'B' and (resid 450 through 491 )B450 - 491
9X-RAY DIFFRACTION9chain 'B' and (resid 492 through 563 )B492 - 563
10X-RAY DIFFRACTION10chain 'B' and (resid 564 through 599 )B564 - 599
11X-RAY DIFFRACTION11chain 'B' and (resid 600 through 646 )B600 - 646

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