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- PDB-2bbs: Human deltaF508 NBD1 with three solubilizing mutations -

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Basic information

Entry
Database: PDB / ID: 2bbs
TitleHuman deltaF508 NBD1 with three solubilizing mutations
ComponentsCystic fibrosis transmembrane conductance regulator
KeywordsTRANSPORT PROTEIN / ATP Binding Cassette
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 / membrane hyperpolarization / cholesterol transport / bicarbonate transport / 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 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 / isomerase activity / chloride transmembrane transport / 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 / 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: 2.05 Å
AuthorsLewis, H.A. / Kearins, M.C. / Conners, K. / Zhao, X. / Lu, F. / Sauder, J.M. / Emtage, S.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: Structure and dynamics of NBD1 from CFTR characterized using crystallography and hydrogen/deuterium exchange mass spectrometry.
Authors: Lewis, H.A. / Wang, C. / Zhao, X. / Hamuro, Y. / Conners, K. / Kearins, M.C. / Lu, F. / Sauder, J.M. / Molnar, K.S. / Coales, S.J. / Maloney, P.C. / Guggino, W.B. / Wetmore, D.R. / Weber, P.C. / Hunt, J.F.
History
DepositionOct 17, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 1, 2005Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Nov 14, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.5Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)65,8306
Polymers64,7682
Non-polymers1,0634
Water5,639313
1
A: Cystic fibrosis transmembrane conductance regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,9153
Polymers32,3841
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)32,9153
Polymers32,3841
Non-polymers5312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.937, 66.225, 122.531
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


Mass: 32383.752 Da / Num. of mol.: 2 / Fragment: residues 389-678 / Mutation: F429S, F494N, Q636R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CFTR, ABCC7 / Plasmid: pET26b-derived / 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.: 313 / 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: 1.96 Å3/Da / Density % sol: 36.65 %
Crystal growTemperature: 280 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 39% PEG4000, 0.1M LiCl, 50mM Tris, pH 9.0, 3mM ATP, 5mM MgCl2, 2mM TCEP, VAPOR DIFFUSION, HANGING DROP, temperature 280K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97931 Å
DetectorDate: Feb 11, 2005
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 2.05→28.82 Å / Num. obs: 31918 / Observed criterion σ(F): 0 / Observed criterion σ(I): -4

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Processing

Software
NameVersionClassification
MAR345data collection
SCALAdata scaling
MOLREPphasing
REFMAC5refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1XMJ

1xmj


Resolution: 2.05→24.93 Å / Isotropic thermal model: isotropic / Cross valid method: FREE R-VALUE / σ(F): 0 / Stereochemistry target values: Engh-Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2913 1608 -random
Rwork0.2225 ---
all0.226 31918 --
obs0.226 31918 97 %-
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: 27.969 Å2
Baniso -1Baniso -2Baniso -3
1-1.318 Å20 Å20 Å2
2---0.531 Å20 Å2
3----0.787 Å2
Refinement stepCycle: LAST / Resolution: 2.05→24.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3825 0 64 313 4202
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_refined_d0.011
X-RAY DIFFRACTIONr_angle_refined_deg1.384
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.54
X-RAY DIFFRACTIONr_chiral_restr0.092
X-RAY DIFFRACTIONr_gen_planes_refined0.004
X-RAY DIFFRACTIONr_mcbond_it0.951
X-RAY DIFFRACTIONr_mcangle_it1.688
X-RAY DIFFRACTIONr_scbond_it1.929
X-RAY DIFFRACTIONr_scangle_it3.03

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