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- PDB-5d3f: Crystal structure of human 14-3-3 zeta in complex with CFTR R-dom... -

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Basic information

Entry
Database: PDB / ID: 5d3f
TitleCrystal structure of human 14-3-3 zeta in complex with CFTR R-domain peptide pS753-pS768 and stabilizer fusicoccin-A
Components
  • 14-3-3 protein zeta/delta
  • Cystic fibrosis transmembrane conductance regulator
KeywordsSIGNALING PROTEIN / protein-peptide complex / phosphorylation / tandem binding / stabilization / fusicoccin-A / Structural Genomics / Eindhoven University of Technology
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 / synaptic target recognition / positive regulation of enamel mineralization / Golgi reassembly / transepithelial water transport / RHO GTPases regulate CFTR trafficking ...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 / synaptic target recognition / positive regulation of enamel mineralization / Golgi reassembly / transepithelial water transport / RHO GTPases regulate CFTR trafficking / intracellular pH elevation / amelogenesis / chloride channel inhibitor activity / NOTCH4 Activation and Transmission of Signal to the Nucleus / ATPase-coupled inorganic anion transmembrane transporter activity / establishment of Golgi localization / Golgi-associated vesicle membrane / multicellular organismal-level water homeostasis / respiratory system process / tube formation / cholesterol transport / regulation of synapse maturation / Rap1 signalling / bicarbonate transport / bicarbonate transmembrane transporter activity / chloride channel regulator activity / membrane hyperpolarization / vesicle docking involved in exocytosis / negative regulation of protein localization to nucleus / chloride transmembrane transporter activity / KSRP (KHSRP) binds and destabilizes mRNA / GP1b-IX-V activation signalling / sperm capacitation / cholesterol biosynthetic process / RHOQ GTPase cycle / chloride channel activity / positive regulation of exocytosis / Regulation of localization of FOXO transcription factors / Interleukin-3, Interleukin-5 and GM-CSF signaling / phosphoserine residue binding / ATPase-coupled transmembrane transporter activity / Activation of BAD and translocation to mitochondria / ABC-type transporter activity / positive regulation of insulin secretion involved in cellular response to glucose stimulus / chloride channel complex / protein targeting / regulation of ERK1 and ERK2 cascade / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / cellular response to glucose starvation / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / RHO GTPases activate PKNs / negative regulation of TORC1 signaling / cellular response to cAMP / ERK1 and ERK2 cascade / 14-3-3 protein binding / Transcriptional and post-translational regulation of MITF-M expression and activity / cellular response to forskolin / protein sequestering activity / negative regulation of innate immune response / chloride transmembrane transport / response to endoplasmic reticulum stress / hippocampal mossy fiber to CA3 synapse / PDZ domain binding / Translocation of SLC2A4 (GLUT4) to the plasma membrane / TP53 Regulates Metabolic Genes / Deactivation of the beta-catenin transactivating complex / lung development / establishment of localization in cell / clathrin-coated endocytic vesicle membrane / Defective CFTR causes cystic fibrosis / Negative regulation of NOTCH4 signaling / Late endosomal microautophagy / recycling endosome / regulation of protein stability / ABC-family proteins mediated transport / transmembrane transport / recycling endosome membrane / Chaperone Mediated Autophagy / Aggrephagy / melanosome / intracellular protein localization / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / protein-folding chaperone binding / early endosome membrane / angiogenesis / protein phosphatase binding / blood microparticle / vesicle / DNA-binding transcription factor binding / transmembrane transporter binding / early endosome / endosome membrane / Ub-specific processing proteases / protein phosphorylation / cadherin binding / apical plasma membrane / protein domain specific binding / lysosomal membrane
Similarity search - Function
: / CFTR regulator domain / Cystic fibrosis TM conductance regulator (CFTR), regulator domain / Cystic fibrosis transmembrane conductance regulator / : / 14-3-3 domain / Delta-Endotoxin; domain 1 / 14-3-3 proteins signature 2. / 14-3-3 protein, conserved site / 14-3-3 proteins signature 1. ...: / CFTR regulator domain / Cystic fibrosis TM conductance regulator (CFTR), regulator domain / Cystic fibrosis transmembrane conductance regulator / : / 14-3-3 domain / Delta-Endotoxin; domain 1 / 14-3-3 proteins signature 2. / 14-3-3 protein, conserved site / 14-3-3 proteins signature 1. / 14-3-3 protein / 14-3-3 homologues / 14-3-3 domain / 14-3-3 domain superfamily / 14-3-3 protein / 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. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / Mainly Alpha
Similarity search - Domain/homology
FUSICOCCIN / Cystic fibrosis transmembrane conductance regulator / 14-3-3 protein zeta/delta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.74 Å
AuthorsStevers, L.M. / Leysen, S.F.R. / Ottmann, C.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2016
Title: Characterization and small-molecule stabilization of the multisite tandem binding between 14-3-3 and the R domain of CFTR.
Authors: Stevers, L.M. / Lam, C.V. / Leysen, S.F. / Meijer, F.A. / van Scheppingen, D.S. / de Vries, R.M. / Carlile, G.W. / Milroy, L.G. / Thomas, D.Y. / Brunsveld, L. / Ottmann, C.
History
DepositionAug 6, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Mar 16, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2019Group: Advisory / Data collection / Derived calculations
Category: diffrn_radiation_wavelength / pdbx_struct_assembly_gen ...diffrn_radiation_wavelength / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / pdbx_unobs_or_zero_occ_atoms
Item: _pdbx_struct_assembly_prop.value
Revision 1.2Nov 6, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 14-3-3 protein zeta/delta
B: 14-3-3 protein zeta/delta
C: Cystic fibrosis transmembrane conductance regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,5714
Polymers55,8903
Non-polymers6811
Water00
1
A: 14-3-3 protein zeta/delta
C: Cystic fibrosis transmembrane conductance regulator

B: 14-3-3 protein zeta/delta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,5714
Polymers55,8903
Non-polymers6811
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area4110 Å2
ΔGint-21 kcal/mol
Surface area22550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.607, 110.166, 132.604
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein 14-3-3 protein zeta/delta / Protein kinase C inhibitor protein 1 / KCIP-1


Mass: 26316.764 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: YWHAZ / Production host: Escherichia coli (E. coli) / References: UniProt: P63104
#2: Protein/peptide Cystic fibrosis transmembrane conductance regulator / CFTR / ATP-binding cassette sub-family C member 7 / Channel conductance-controlling ATPase / cAMP- ...CFTR / ATP-binding cassette sub-family C member 7 / Channel conductance-controlling ATPase / cAMP-dependent chloride channel


Mass: 3256.653 Da / Num. of mol.: 1 / Fragment: UNP residues 747-774 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P13569, EC: 3.6.3.49
#3: Chemical ChemComp-FSC / FUSICOCCIN


Mass: 680.823 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C36H56O12
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: 2.29 Å3/Da / Density % sol: 46.25 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: HEPES, NaCl, DTT, PEG6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.97886 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Dec 12, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97886 Å / Relative weight: 1
ReflectionRedundancy: 5.8 % / Number: 77328 / Rmerge(I) obs: 0.074 / D res high: 2.74 Å / D res low: 44.2 Å / Num. obs: 13354 / % possible obs: 96.9 / Rejects: 21
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)IDRmerge(I) obsRedundancy
2.742.8710.3054.7
9.0944.210.0575.2
ReflectionResolution: 2.74→44.2 Å / Num. obs: 13354 / % possible obs: 96.9 % / Redundancy: 5.8 % / Biso Wilson estimate: 60.42 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.034 / Net I/σ(I): 13.7 / Num. measured all: 77328 / Scaling rejects: 21
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
2.74-2.874.70.3054.1666314080.9440.14878.7
9.09-44.25.20.05723.122004220.9960.02898.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
Aimless0.3.11data scaling
MOLREPphasing
PDB_EXTRACT3.15data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.74→44.011 Å / SU ML: 0.42 / Cross valid method: NONE / σ(F): 1.35 / Phase error: 34.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3026 606 4.56 %
Rwork0.2457 --
obs0.2483 13280 96.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.74→44.011 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3606 0 48 0 3654
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113704
X-RAY DIFFRACTIONf_angle_d1.385015
X-RAY DIFFRACTIONf_dihedral_angle_d15.951367
X-RAY DIFFRACTIONf_chiral_restr0.061579
X-RAY DIFFRACTIONf_plane_restr0.007638
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7404-3.01610.40651510.3512804X-RAY DIFFRACTION87
3.0161-3.45240.38131260.31133268X-RAY DIFFRACTION100
3.4524-4.34910.29681590.24743258X-RAY DIFFRACTION100
4.3491-44.01660.26371700.20433344X-RAY DIFFRACTION99

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