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- PDB-6gjs: Human NBD1 of CFTR in complex with nanobodies D12 and T4 -

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Basic information

Entry
Database: PDB / ID: 6gjs
TitleHuman NBD1 of CFTR in complex with nanobodies D12 and T4
Components
  • Cystic fibrosis transmembrane conductance regulator
  • Nanobody D12
  • Nanobody T4
KeywordsIMMUNE SYSTEM / 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 / 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 / Cystic fibrosis transmembrane conductance regulator
Similarity search - Component
Biological speciesHomo sapiens (human)
Lama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 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 26, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: 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 / pdbx_struct_conn_angle / struct_conn
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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id
Revision 1.2Nov 13, 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 D12
C: Nanobody T4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,8436
Polymers57,2873
Non-polymers5563
Water7,674426
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4380 Å2
ΔGint-39 kcal/mol
Surface area20090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)152.200, 41.600, 99.300
Angle α, β, γ (deg.)90.00, 120.56, 90.00
Int Tables number5
Space group name H-MC121

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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: 25525.408 Da / Num. of mol.: 1 / Mutation: del405-435
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 D12


Mass: 16273.939 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 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)

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Non-polymers , 3 types, 429 molecules

#4: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 426 / 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: 2.62 Å3/Da / Density % sol: 53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1M SPG pH 4.0, 25 % PEG 1500

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9789 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 1.95→42.6 Å / Num. obs: 39029 / % possible obs: 98.61 % / Redundancy: 3.7 % / Biso Wilson estimate: 29.83 Å2 / Rmerge(I) obs: 0.07603 / Rrim(I) all: 0.08915 / Net I/σ(I): 11.82
Reflection shellResolution: 1.95→2.02 Å / Rmerge(I) obs: 0.584 / Rrim(I) all: 0.6811

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Processing

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

2bbo


Resolution: 1.95→42.6 Å / Cor.coef. Fo:Fc: 0.9567 / Cor.coef. Fo:Fc free: 0.9404 / SU R Cruickshank DPI: 0.143 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.153 / SU Rfree Blow DPI: 0.136 / SU Rfree Cruickshank DPI: 0.132
RfactorNum. reflection% reflectionSelection details
Rfree0.2123 1952 5 %RANDOM
Rwork0.1773 ---
obs0.1791 39026 98.61 %-
Displacement parametersBiso mean: 35.53 Å2
Baniso -1Baniso -2Baniso -3
1-2.014 Å20 Å2-0.7952 Å2
2---3.5327 Å20 Å2
3---1.5188 Å2
Refine analyzeLuzzati coordinate error obs: 0.255 Å
Refinement stepCycle: 1 / Resolution: 1.95→42.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3492 0 33 429 3954
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013586HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.124862HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1245SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes85HARMONIC2
X-RAY DIFFRACTIONt_gen_planes542HARMONIC5
X-RAY DIFFRACTIONt_it3586HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.53
X-RAY DIFFRACTIONt_other_torsion17.41
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion480SEMIHARMONIC5
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_contact4468SEMIHARMONIC4
LS refinement shellResolution: 1.95→2 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2912 139 5.03 %
Rwork0.2407 2627 -
all0.2433 2766 -
obs--98.61 %
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)
11.9493-0.38110.2961.11470.12231.0823-0.04650.1844-0.0316-0.08370.02480.0356-0.10440.0840.0217-0.01-0.05750.0002-0.0776-0.0006-0.06623.96216.219830.2296
21.53380.0671-0.58430.2705-1.11122.12280.0770.11750.0280.04430.1023-0.0093-0.07640.051-0.1793-0.0257-0.08470.03490.1124-0.0616-0.176440.980310.47229.5925
32.058-0.267-0.92041.25620.42570.7822-0.065-0.11870.0889-0.00630.09320.036-0.0366-0.0361-0.0281-0.06080.0129-0.027-0.00860.03-0.021737.241412.5451.2213
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }

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