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- PDB-6gjq: human NBD1 of CFTR in complex with nanobody T27 -

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Basic information

Entry
Database: PDB / ID: 6gjq
Titlehuman NBD1 of CFTR in complex with nanobody T27
Components
  • Cystic fibrosis transmembrane conductance regulator
  • Nanobody T27
KeywordsHYDROLASE / Cystic Fibrosis / CFTR / nanobodies / thermal stabilization / conformational dynamics
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 / vesicle docking involved in exocytosis / 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 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 forskolin / cellular response to cAMP / chloride transmembrane transport / 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 / Cystic fibrosis transmembrane conductance regulator
Similarity search - Component
Biological speciesHomo sapiens (human)
Lama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.49 Å
AuthorsSigoillot, M. / Overtus, M. / Grodecka, M. / Scholl, D. / Garcia-Pino, A. / Laeremans, T. / He, L. / Pardon, E. / Hildebrandt, E. / Urbatsch, I. ...Sigoillot, M. / Overtus, M. / Grodecka, M. / Scholl, D. / Garcia-Pino, A. / Laeremans, T. / He, L. / Pardon, E. / Hildebrandt, E. / Urbatsch, I. / Steyaert, J. / Riordan, J.R. / Govaerts, C.
CitationJournal: Nat Commun / Year: 2019
Title: Domain-interface dynamics of CFTR revealed by stabilizing nanobodies.
Authors: Sigoillot, M. / Overtus, M. / Grodecka, M. / Scholl, D. / Garcia-Pino, A. / Laeremans, T. / He, L. / Pardon, E. / Hildebrandt, E. / Urbatsch, I. / Steyaert, J. / Riordan, J.R. / Govaerts, C.
History
DepositionMay 16, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 19, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Aug 21, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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: Nanobody T27
C: Cystic fibrosis transmembrane conductance regulator
D: Nanobody T27
E: Cystic fibrosis transmembrane conductance regulator
F: Nanobody T27
G: Cystic fibrosis transmembrane conductance regulator
H: Nanobody T27
hetero molecules


Theoretical massNumber of molelcules
Total (without water)182,54812
Polymers180,5208
Non-polymers2,0294
Water8,089449
1
A: Cystic fibrosis transmembrane conductance regulator
B: Nanobody T27
E: Cystic fibrosis transmembrane conductance regulator
F: Nanobody T27
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,2746
Polymers90,2604
Non-polymers1,0142
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6870 Å2
ΔGint-42 kcal/mol
Surface area27320 Å2
MethodPISA
2
C: Cystic fibrosis transmembrane conductance regulator
D: Nanobody T27
hetero molecules

G: Cystic fibrosis transmembrane conductance regulator
H: Nanobody T27
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,2746
Polymers90,2604
Non-polymers1,0142
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_554-x+1/2,-y,z-1/21
Buried area6850 Å2
ΔGint-41 kcal/mol
Surface area27300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.490, 118.150, 180.210
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Cystic fibrosis transmembrane conductance regulator / ATP-binding cassette sub-family C member 7 / Channel conductance-controlling ATPase / cAMP- ...ATP-binding cassette sub-family C member 7 / Channel conductance-controlling ATPase / cAMP-dependent chloride channel


Mass: 29218.408 Da / Num. of mol.: 4 / Mutation: S492P, A534P, I539T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CFTR / Production host: Escherichia coli (E. coli)
References: UniProt: Q20BJ8, UniProt: P13569*PLUS, EC: 3.6.3.49
#2: Antibody
Nanobody T27


Mass: 15911.473 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli)
#3: 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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 449 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.24 Å3/Da / Density % sol: 45.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Lithium sulfate monohydrate, 0.1 M BIS-TRIS pH 6.5, 25% w/v Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 28, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.49→49.4 Å / Num. obs: 48671 / % possible obs: 99.18 % / Redundancy: 9.15 % / Biso Wilson estimate: 70.66 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.1819 / Rrim(I) all: 0.193 / Net I/σ(I): 10.35
Reflection shellResolution: 2.49→2.56 Å / Rmerge(I) obs: 0.64 / CC1/2: 0.467 / Rrim(I) all: 1.741

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Processing

Software
NameVersionClassification
BUSTER2.10.1refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementResolution: 2.49→47.93 Å / Cor.coef. Fo:Fc: 0.9337 / Cor.coef. Fo:Fc free: 0.9073 / SU R Cruickshank DPI: 0.544 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.61 / SU Rfree Blow DPI: 0.272 / SU Rfree Cruickshank DPI: 0.271
RfactorNum. reflection% reflectionSelection details
Rfree0.2396 2433 5 %RANDOM
Rwork0.1985 ---
obs0.2005 48669 99.18 %-
Displacement parametersBiso mean: 51.28 Å2
Baniso -1Baniso -2Baniso -3
1-0.5126 Å20 Å20 Å2
2---3.7887 Å20 Å2
3---3.2761 Å2
Refine analyzeLuzzati coordinate error obs: 0.315 Å
Refinement stepCycle: 1 / Resolution: 2.49→47.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9511 0 124 453 10088
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.019819HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.2413284HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3412SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes221HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1477HARMONIC5
X-RAY DIFFRACTIONt_it9819HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.37
X-RAY DIFFRACTIONt_other_torsion19.3
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1271SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact10854SEMIHARMONIC4
LS refinement shellResolution: 2.49→2.56 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.317 157 5 %
Rwork0.2422 2984 -
all0.2459 3141 -
obs--99.18 %

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