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- PDB-6uk1: Crystal structure of nucleotide-binding domain 2 (NBD2) of the hu... -

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Basic information

Entry
Database: PDB / ID: 6uk1
TitleCrystal structure of nucleotide-binding domain 2 (NBD2) of the human Cystic Fibrosis Transmembrane Conductance Regulator (CFTR)
ComponentsCystic fibrosis transmembrane conductance regulator
KeywordsHYDROLASE / NBD2 / CFTR / ABC transport
Function / homology
Function and homology information


positive regulation of voltage-gated chloride 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 / amelogenesis / intracellular pH elevation ...positive regulation of voltage-gated chloride 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 / amelogenesis / intracellular pH elevation / chloride channel inhibitor activity / : / Golgi-associated vesicle membrane / multicellular organismal-level water homeostasis / cholesterol transport / bicarbonate transport / bicarbonate transmembrane transporter activity / vesicle docking involved in exocytosis / chloride channel regulator activity / membrane hyperpolarization / chloride transmembrane transporter activity / sperm capacitation / cholesterol biosynthetic process / RHOQ GTPase cycle / chloride channel activity / positive regulation of exocytosis / ATPase-coupled transmembrane transporter activity / chloride channel complex / positive regulation of insulin secretion involved in cellular response to glucose stimulus / ABC-type transporter activity / 14-3-3 protein binding / cellular response to forskolin / chloride transmembrane transport / response to endoplasmic reticulum stress / cellular response to cAMP / PDZ domain binding / establishment of localization in cell / clathrin-coated endocytic vesicle membrane / Defective CFTR causes cystic fibrosis / 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 / 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 ...: / 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: 2.693 Å
AuthorsWang, C. / Vorobiev, S.M. / Vernon, R.M. / Khazanov, N. / Senderowitz, H. / Forman-Kay, J.D. / Hunt, J.F.
Funding support United States, 1items
OrganizationGrant numberCountry
Cystic Fibrosis FoundationHUNT13XX0 United States
Citation
Journal: To Be Published
Title: A thermodynamically stabilized form of the second nucleotide binding domain from human CFTR shows a catalytically inactive conformation
Authors: Wang, C. / Vorobiev, S. / Vernon, R.M. / Khazanov, N. / Senderowitz, H. / Forman-Kay, J.D. / Hunt, J.F.
#1: Journal: To Be Published
Title: Mutational stabilization of the second nucleotide binding domain (NBD2) of CFTR yields soluble protein and insight into NBD2 disease-causing mutations
Authors: Vernon, R.M. / Chong, P.A. / Lin, H. / Yang, Z. / Zhou, Q. / Aleksandrov, A.A. / An, J. / Protasevich, I. / Dawson, J.E. / Riordan, J.R. / Thibodeau, P.H. / Brouillette, C.G. / Forman-Kay, J.D.
History
DepositionOct 3, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 7, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 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
B: Cystic fibrosis transmembrane conductance regulator
C: Cystic fibrosis transmembrane conductance regulator
D: Cystic fibrosis transmembrane conductance regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,33512
Polymers102,2094
Non-polymers2,1268
Water1,33374
1
A: Cystic fibrosis transmembrane conductance regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,0843
Polymers25,5521
Non-polymers5312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Cystic fibrosis transmembrane conductance regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,0843
Polymers25,5521
Non-polymers5312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Cystic fibrosis transmembrane conductance regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,0843
Polymers25,5521
Non-polymers5312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Cystic fibrosis transmembrane conductance regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,0843
Polymers25,5521
Non-polymers5312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)95.063, 60.132, 105.160
Angle α, β, γ (deg.)90.000, 99.570, 90.000
Int Tables number4
Space group name H-MP1211

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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: 25552.297 Da / Num. of mol.: 4
Mutation: S1255L,Q1280E,K1292D,Y1307N,K1334G,S1359A,Q1411D,H1402A,Q1411D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CFTR, ABCC7 / Production host: Escherichia coli (E. coli)
References: UniProt: P13569, channel-conductance-controlling ATPase
#2: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 4 / 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.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 74 / 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: 2.9 Å3/Da / Density % sol: 57.58 %
Crystal growTemperature: 277 K / Method: microbatch
Details: 24% PEG 8000, 100 mM Li2SO4, 10mM NaBr, 100 mM Bis-Tris Propane pH 6.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 14, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.693→100 Å / Num. obs: 32360 / % possible obs: 99 % / Redundancy: 5 % / Rpim(I) all: 0.05 / Rrim(I) all: 0.116 / Net I/σ(I): 17.1
Reflection shellResolution: 2.7→5.98 Å / Num. unique obs: 28962 / Rpim(I) all: 0.05 / Rrim(I) all: 0.116

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3GD7

3gd7


Resolution: 2.693→64.414 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 41.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3036 1552 4.82 %
Rwork0.2734 30651 -
obs0.2749 32203 98.12 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 122.42 Å2 / Biso mean: 52.7125 Å2 / Biso min: 5.03 Å2
Refinement stepCycle: final / Resolution: 2.693→64.414 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7021 0 128 74 7223
Biso mean--36.67 35.84 -
Num. residues----912
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.6932-2.78010.40941360.3211256393
2.7801-2.87950.34671330.3137280998
2.8795-2.99470.35681300.3184276298
2.9947-3.1310.29941570.2921274098
3.131-3.29610.29381380.2863278099
3.2961-3.50260.31311430.2771282499
3.5026-3.7730.30441540.26342797100
3.773-4.15260.28521360.25752829100
4.1526-4.75340.31411480.24112844100
4.7534-5.98810.3181420.27052860100
5.9881-64.4140.24471350.2733284396
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)
10.00780.0098-0.01530.0286-0.01290.0117-0.04040.0469-0.1076-0.05290.06250.00410.2145-0.06250.06370.3129-0.090.1263-0.19050.1343-0.1752-5.4222-4.996631.8419
20.0063-0.00420.00110.0207-0.00360.0020.0201-0.00240.02980.0292-0.01530.04290.09470.0933-0.01010.22620.11030.1027-0.1402-0.06240.01861.3697.872654.1351
30.03840.0209-0.05930.0202-0.04210.0931-0.148-0.0603-0.0264-0.0561-0.0325-0.05210.15490.0065-0.2378-0.11880.1604-0.0657-0.3292-0.2766-0.35489.1592-0.698732.0173
40.02840.0014-0.02050.0367-0.02720.0363-0.1792-0.0693-0.03590.0415-0.0227-0.07410.07670.1183-0.13160.22240.3070.06740.80980.06790.87844.1564-5.05119.9844
50.00720.0059-0.00380.0079-0.00730.0192-0.0335-0.01360.0348-0.0288-0.0623-0.1330.04930.0321-00.6914-0.30520.23711.4047-0.07750.926537.73528.22-4.0108
60.0090.0099-0.00630.0183-0.00760.0053-0.1670.0766-0.1586-0.01220.136-0.11130.06020.0651-00.3796-0.03090.13840.9795-0.02390.90830.86180.795116.8303
70.00690.01720.01780.03660.04970.05080.0079-0.0128-0.0923-0.07150.0166-0.10050.0336-0.0274-0.04180.3743-0.2354-0.26960.6239-0.16330.713841.537934.239434.7233
80.1260.03590.05350.0339-0.00390.04940.01110.014-0.0139-0.0143-0.0654-0.0902-0.06640.123-0.07640.4067-0.1508-0.35581.0902-0.17910.947844.007827.357329.5715
90.003-0.00340.00250.001-0.00190.00370.0531-0.0681-0.03530.02960.0608-0.0123-0.02640.036600.8540.0632-0.25641.1473-0.03680.894738.411720.642544.1275
100.04740.00870.03420.0561-0.00680.02220.0133-0.12630.00320.0848-0.0257-0.0894-0.0509-0.03080.02740.24360.2414-0.22090.98590.01080.693827.439617.047747.6861
110.0323-0.0271-0.02330.02270.01340.0517-0.0255-0.0830.0323-0.07310.0749-0.0029-0.0898-0.0190.04250.3111-0.0447-0.25410.5778-0.22470.755428.475925.97425.6382
120.0130.027-0.04090.051-0.04850.05250.07170.05750.1771-0.00720.0280.0832-0.2007-0.09420.21910.02520.01650.2475-0.3580.1591-0.3306-4.823128.406621.8907
130.14380.0508-0.00830.0144-0.0020.0004-0.00820.0871-0.0429-0.01520.0314-0.0077-0.06150.03110.04630.2005-0.0048-0.01730.1584-0.01680.11950.350820.40237.8125
140.09420.02340.09260.0170.02720.09620.07870.0739-0.0601-0.0680.0320.01230.00420.15860.09350.5695-0.1742-0.01220.2492-0.0785-0.025612.43816.09860.7743
150.05670.0034-0.01420.0351-0.02790.0202-0.01760.01550.12670.12170.0149-0.028-0.13720.0806-0.04420.1685-0.0092-0.0536-0.1649-0.214-0.07059.671924.790224.2909
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1202 through 1289 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 1290 through 1362 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 1363 through 1430 )A0
4X-RAY DIFFRACTION4chain 'B' and (resid 1202 through 1289 )B0
5X-RAY DIFFRACTION5chain 'B' and (resid 1290 through 1347 )B0
6X-RAY DIFFRACTION6chain 'B' and (resid 1348 through 1430 )B0
7X-RAY DIFFRACTION7chain 'C' and (resid 1202 through 1218 )C0
8X-RAY DIFFRACTION8chain 'C' and (resid 1219 through 1278 )C0
9X-RAY DIFFRACTION9chain 'C' and (resid 1279 through 1299 )C0
10X-RAY DIFFRACTION10chain 'C' and (resid 1300 through 1377 )C0
11X-RAY DIFFRACTION11chain 'C' and (resid 1378 through 1430 )C0
12X-RAY DIFFRACTION12chain 'D' and (resid 1204 through 1278 )D0
13X-RAY DIFFRACTION13chain 'D' and (resid 1279 through 1299 )D0
14X-RAY DIFFRACTION14chain 'D' and (resid 1300 through 1361 )D0
15X-RAY DIFFRACTION15chain 'D' and (resid 1362 through 1429 )D0

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