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- PDB-2pze: Minimal human CFTR first nucleotide binding domain as a head-to-t... -

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Basic information

Entry
Database: PDB / ID: 2pze
TitleMinimal human CFTR first nucleotide binding domain as a head-to-tail dimer
ComponentsCystic fibrosis transmembrane conductance regulator
KeywordsHYDROLASE / NBD / ABC transporter / CFTR
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 / ATPase-coupled inorganic anion transmembrane transporter activity ...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 / ATPase-coupled inorganic anion transmembrane transporter activity / amelogenesis / chloride channel inhibitor activity / Golgi-associated vesicle membrane / multicellular organismal-level water homeostasis / vesicle docking involved in exocytosis / cholesterol transport / membrane hyperpolarization / bicarbonate transmembrane transporter activity / bicarbonate transport / chloride channel regulator activity / chloride transmembrane transporter activity / sperm capacitation / chloride channel activity / cholesterol biosynthetic process / RHOQ GTPase cycle / 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 forskolin / cellular response to cAMP / isomerase activity / chloride transmembrane transport / response to endoplasmic reticulum stress / PDZ domain binding / establishment of localization in cell / Defective CFTR causes cystic fibrosis / clathrin-coated endocytic vesicle membrane / Late endosomal microautophagy / 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 / 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. / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 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: 1.7 Å
AuthorsAtwell, S. / Conners, K. / Emtage, S. / Gheyi, T. / Glenn, N.R. / Hendle, J. / Lewis, H.A. / Lu, F. / Rodgers, L.A. / Romero, R. ...Atwell, S. / Conners, K. / Emtage, S. / Gheyi, T. / Glenn, N.R. / Hendle, J. / Lewis, H.A. / Lu, F. / Rodgers, L.A. / Romero, R. / Sauder, J.M. / Smith, D. / Tien, H. / Wasserman, S.R. / Zhao, X.
Citation
Journal: Protein Eng.Des.Sel. / Year: 2010
Title: Structures of a minimal human CFTR first nucleotide-binding domain as a monomer, head-to-tail homodimer, and pathogenic mutant.
Authors: Atwell, S. / Brouillette, C.G. / Conners, K. / Emtage, S. / Gheyi, T. / Guggino, W.B. / Hendle, J. / Hunt, J.F. / Lewis, H.A. / Lu, F. / Protasevich, I.I. / Rodgers, L.A. / Romero, R. / ...Authors: Atwell, S. / Brouillette, C.G. / Conners, K. / Emtage, S. / Gheyi, T. / Guggino, W.B. / Hendle, J. / Hunt, J.F. / Lewis, H.A. / Lu, F. / Protasevich, I.I. / Rodgers, L.A. / Romero, R. / Wasserman, S.R. / Weber, P.C. / Wetmore, D. / Zhang, F.F. / Zhao, X.
#1: Journal: Pediatr.Pulmonol.Suppl. / Year: 2007
Title: Structure of the human CFTR NBD1 domain as a homodimer: insights and applications
Authors: Atwell, S. / Conners, K. / Emtage, S. / Gheyi, T. / Lewis, H. / Lu, F. / Romero, R. / Zhao, X.
History
DepositionMay 17, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 9, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 16, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Nov 14, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.5Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,1146
Polymers51,0512
Non-polymers1,0634
Water3,495194
1
A: Cystic fibrosis transmembrane conductance regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,0573
Polymers25,5251
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)26,0573
Polymers25,5251
Non-polymers5312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.803, 92.779, 107.419
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 / cAMP- dependent chloride channel / ATP-binding cassette transporter sub- family C member 7


Mass: 25525.408 Da / Num. of mol.: 2 / Fragment: CFTR NBD1 387-646(del405-436) / Mutation: del405-436
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CFTR, ABCC7 / Plasmid: modified pET26b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) codon+RIL / References: UniProt: P13569
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 194 / 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: 2.09 Å3/Da / Density % sol: 41.11 %
Crystal growTemperature: 281 K / Method: vapor diffusion / pH: 7.5
Details: Protein: 9.5mg/ml NBD1, 0.15M NaCl, 0.01M methionine, 0.01M HEPES pH 7.5, 10% glycerol, 0.001M TCEP, 0.002M ATP; Well: 0.1M Hepes pH 7.5, 25% PEG 6K; Cryo: 25% DMSO, vapor diffusion, temperature 281K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9796 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Dec 13, 2006 / Details: mirrors
RadiationMonochromator: diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 1.7→22.094 Å / Num. all: 47121 / Num. obs: 47121 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 20.6 Å2 / Rmerge(I) obs: 0.086 / Rsym value: 0.086 / Net I/σ(I): 5.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.7-1.793.60.7490.82463267960.74998.6
1.79-1.93.70.4521.42353064390.45299
1.9-2.033.70.2512.22239860990.25199.2
2.03-2.193.70.1583.92106056920.15899.6
2.19-2.43.70.1115.71957653000.11199.7
2.4-2.693.70.0876.91776448020.08799.5
2.69-3.13.70.0678.91562242110.06799.3
3.1-3.83.70.0589.71326335740.05898.6
3.8-5.383.70.05211.31022827520.05296.4
5.38-22.093.60.04712.2524814560.04790

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
REFMACrefinement
PDB_EXTRACT2data extraction
MAR345data collection
MOSFLMdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1XMI

1xmi


Resolution: 1.7→21.296 Å / Isotropic thermal model: isotropic / Cross valid method: FREE R-VALUE / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2468 2405 -RANDOM
Rwork0.2101 ---
all0.212 47005 --
obs0.212 47005 98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: Mask bulk solvent correction
Displacement parametersBiso mean: 23.89 Å2
Baniso -1Baniso -2Baniso -3
1-0.825 Å20 Å20 Å2
2---0.187 Å20 Å2
3----0.639 Å2
Refinement stepCycle: LAST / Resolution: 1.7→21.296 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3342 0 64 194 3600
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.01
X-RAY DIFFRACTIONr_angle_d1.358
X-RAY DIFFRACTIONr_planar_tor5.601
X-RAY DIFFRACTIONr_chiral_restr0.085
X-RAY DIFFRACTIONr_plane_restr0.005
X-RAY DIFFRACTIONr_mcbond_it1.182
X-RAY DIFFRACTIONr_mcangle_it2.137
X-RAY DIFFRACTIONr_scbond_it3.056
X-RAY DIFFRACTIONr_scangle_it4.438

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