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- PDB-6gju: human NBD1 of CFTR in complex with nanobodies T2a and T4 -

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Basic information

Entry
Database: PDB / ID: 6gju
Titlehuman NBD1 of CFTR in complex with nanobodies T2a and T4
Components
  • Cystic fibrosis transmembrane conductance regulator
  • Nanobody T2a
  • Nanobody T4
KeywordsHYDROLASE / Cystic Fibrosis / CFTR / nanobodies / thermal stabilization / conformational dynamics
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 / regulation of biological quality / amelogenesis ...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 / regulation of biological quality / amelogenesis / intracellular pH elevation / chloride channel inhibitor activity / : / multicellular organismal-level water homeostasis / Golgi-associated vesicle membrane / cholesterol transport / bicarbonate transport / bicarbonate transmembrane transporter activity / membrane hyperpolarization / chloride channel regulator activity / vesicle docking involved in exocytosis / chloride transmembrane transporter activity / cholesterol biosynthetic process / sperm capacitation / chloride channel activity / RHOQ GTPase cycle / positive regulation of exocytosis / ATPase-coupled transmembrane transporter activity / positive regulation of insulin secretion involved in cellular response to glucose stimulus / ABC-type transporter activity / chloride channel complex / 14-3-3 protein binding / cellular response to forskolin / chloride transmembrane transport / cellular response to cAMP / response to endoplasmic reticulum stress / PDZ domain binding / clathrin-coated endocytic vesicle membrane / establishment of localization in cell / 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 / protein-folding chaperone binding / Clathrin-mediated endocytosis / 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 / nucleus / membrane / 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
DI(HYDROXYETHYL)ETHER / Cystic fibrosis transmembrane conductance regulator / Cystic fibrosis transmembrane conductance regulator
Similarity search - Component
Biological speciesHomo sapiens (human)
Lama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 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 17, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 26, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 21, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.2Jan 17, 2024Group: 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 / refine
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine.pdbx_diffrn_id
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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 T4
C: Nanobody T2a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,7255
Polymers60,5273
Non-polymers1982
Water1,49583
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4010 Å2
ΔGint-12 kcal/mol
Surface area19240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.680, 135.780, 190.650
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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Protein , 1 types, 1 molecules A

#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.: 1 / 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

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Antibody , 2 types, 2 molecules BC

#2: Antibody Nanobody T4


Mass: 15488.098 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli)
#3: Antibody Nanobody T2a


Mass: 15820.306 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli)

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Non-polymers , 3 types, 85 molecules

#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 83 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.07 Å3/Da / Density % sol: 40.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2M Sodium sulfate, 20% w/v PEG 3350

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 29, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.6→46.4 Å / Num. obs: 17227 / % possible obs: 100 % / Redundancy: 13.1 % / Biso Wilson estimate: 101.67 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.1204 / Rrim(I) all: 0.1311 / Net I/σ(I): 15.39
Reflection shellResolution: 2.6→2.69 Å / Rmerge(I) obs: 0.1204 / Num. unique obs: 16001 / CC1/2: 0.997 / Rrim(I) all: 0.1311

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Processing

Software
NameVersionClassification
BUSTER2.10.1refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2PZE and 1MEL

2pze

1mel


Resolution: 2.6→46.4 Å / Cor.coef. Fo:Fc: 0.9057 / Cor.coef. Fo:Fc free: 0.8988 / SU R Cruickshank DPI: 0.602 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.659 / SU Rfree Blow DPI: 0.285 / SU Rfree Cruickshank DPI: 0.285
RfactorNum. reflection% reflectionSelection details
Rfree0.2435 800 5 %RANDOM
Rwork0.2204 ---
obs0.2216 16001 99.88 %-
Displacement parametersBiso mean: 77.58 Å2
Baniso -1Baniso -2Baniso -3
1-7.3157 Å20 Å20 Å2
2---23.9301 Å20 Å2
3---16.6144 Å2
Refine analyzeLuzzati coordinate error obs: 0.452 Å
Refinement stepCycle: LAST / Resolution: 2.6→46.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3157 0 13 87 3257
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0083230HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.124364HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1092SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes69HARMONIC2
X-RAY DIFFRACTIONt_gen_planes481HARMONIC5
X-RAY DIFFRACTIONt_it3230HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.51
X-RAY DIFFRACTIONt_other_torsion19.26
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion424SEMIHARMONIC5
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_contact3418SEMIHARMONIC4
LS refinement shellResolution: 2.6→2.78 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.4209 142 4.98 %
Rwork0.3121 2707 -
all0.3174 2849 -
obs--99.88 %
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)
10.68740.5692-0.79310-0.57533.8850.0365-0.1291-0.02320.0412-0.0749-0.0262-0.060.01110.0384-0.15440.15420.00670.0179-0.0002-0.1406-5.554-7.05327.1849
21.5021-1.00131.0360.99890.67612.0307-0.0429-0.167-0.00140.0763-0.00820.0691-0.128-0.06430.051-0.0930.08470.0474-0.1198-0.0056-0.0678-11.976511.26249.6785
30.04850.17310.8242.83081.81462.73150.02870.0283-0.0818-0.0444-0.0722-0.08160.1876-0.06360.04350.03190.10270.0907-0.05370.0102-0.234-10.9379-30.56518.2979
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }

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