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- PDB-6gk4: Human NBD1 of CFTR in complex with nanobodies D12 and T8 -

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Basic information

Entry
Database: PDB / ID: 6gk4
TitleHuman NBD1 of CFTR in complex with nanobodies D12 and T8
Components
  • Cystic fibrosis transmembrane conductance regulator
  • Nanobody D12
  • Nanobody T8
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 / MOLECULAR REPLACEMENT / Resolution: 2.91 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 18, 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 1.3Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_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

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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 T8
D: Cystic fibrosis transmembrane conductance regulator
E: Nanobody D12
F: Nanobody T8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,46911
Polymers114,3146
Non-polymers1,1555
Water4,270237
1
A: Cystic fibrosis transmembrane conductance regulator
B: Nanobody D12
C: Nanobody T8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,7816
Polymers57,1573
Non-polymers6243
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4130 Å2
ΔGint-35 kcal/mol
Surface area19210 Å2
MethodPISA
2
D: Cystic fibrosis transmembrane conductance regulator
E: Nanobody D12
F: Nanobody T8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,6895
Polymers57,1573
Non-polymers5312
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3990 Å2
ΔGint-34 kcal/mol
Surface area19140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.940, 55.190, 114.990
Angle α, β, γ (deg.)90.00, 103.96, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AD

#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.: 2 / Mutation: del405-436,del405-436
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, 4 molecules BECF

#2: Antibody Nanobody D12


Mass: 16273.939 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli)
#3: Antibody Nanobody T8


Mass: 15357.844 Da / Num. of mol.: 2
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 , 4 types, 242 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-MG / MAGNESIUM ION


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


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


Mass: 18.015 Da / Num. of mol.: 237 / 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: 2.18 Å3/Da / Density % sol: 43.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.15 M Potassium bromide, 30% w/v Polyethylene glycol monomethyl ether 2,000

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Data collection

DiffractionMean temperature: 100 K
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: 2.91→45.16 Å / Num. obs: 21888 / % possible obs: 99 % / Redundancy: 3.3 % / Biso Wilson estimate: 73.07 Å2 / CC1/2: 0.985 / Rmerge(I) obs: 0.135 / Rrim(I) all: 0.161 / Net I/σ(I): 8.2
Reflection shellResolution: 2.91→3.014 Å / Rmerge(I) obs: 0.592 / CC1/2: 0.62 / Rrim(I) all: 0.703

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Processing

Software
NameVersionClassification
BUSTER2.10.1refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.91→45.16 Å / Cor.coef. Fo:Fc: 0.8416 / Cor.coef. Fo:Fc free: 0.7849 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.434
RfactorNum. reflection% reflectionSelection details
Rfree0.2946 1086 4.96 %RANDOM
Rwork0.2464 ---
obs0.2268 21888 99.45 %-
Displacement parametersBiso mean: 51.78 Å2
Baniso -1Baniso -2Baniso -3
1--12.4909 Å20 Å29.9535 Å2
2--9.9984 Å20 Å2
3---2.4926 Å2
Refine analyzeLuzzati coordinate error obs: 0.409 Å
Refinement stepCycle: 1 / Resolution: 2.91→45.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6575 0 70 237 6882
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0116768HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.219201HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2223SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes141HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1036HARMONIC5
X-RAY DIFFRACTIONt_it6768HARMONIC20
X-RAY DIFFRACTIONt_nbd2SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.56
X-RAY DIFFRACTIONt_other_torsion21.16
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion918SEMIHARMONIC5
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_contact7368SEMIHARMONIC4
LS refinement shellResolution: 2.91→3.05 Å / Total num. of bins used: 11
RfactorNum. reflection% reflection
Rfree0.3657 145 5.02 %
Rwork0.3037 2742 -
all0.2365 2887 -
obs--99.45 %
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)
10.04120.76860.59940.6845-0.83941.08050.00420.0066-0.0174-0.0050.0083-0.0019-0.0048-0.0162-0.01250.023-0.0388-0.0196-0.03160.0292-0.024129.11816.036-56.1021
2-0.6018-0.68531.22720.206-0.80060.9153-0.00170.0069-0.0055-0.00720.0026-0.00190.0050.0003-0.0009-0.00780.0238-0.0266-0.00360.0308-0.010140.305610.7816-32.8338
3-0.27750.42020.68050.39130.25010.61520.0017-0.0039-0.0076-0.0035-0.0054-0.0032-0.00570.00450.00370.027-0.0409-0.032-0.02430.0117-0.022843.360833.803-70.8017
40.76271.0174-0.28840.5559-0.39980.20010.0020.0203-0.00740.00120.010.0173-0.01130.0073-0.0119-0.006-0.0349-0.0027-0.015-0.001-0.008217.303831.3706-14.6801
5-0.76070.33491.57720.3221.36070.83120.00270.00130.01760.00180.00240.0012-0.01460.0079-0.00510.017-0.0178-0.0453-0.0126-0.0519-0.029129.019235.43049.2385
60.16940.11550.0330.0211-0.07630.44670.0042-0.01860.0053-0.0080.00140.0023-0.00340.0024-0.00560.0121-0.00890.00140.00060.0019-0.0051-3.239613.7057-13.4947
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }
4X-RAY DIFFRACTION4{ D|* }
5X-RAY DIFFRACTION5{ E|* }
6X-RAY DIFFRACTION6{ F|* }

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