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- PDB-5d3e: Crystal structure of human 14-3-3 gamma in complex with CFTR R-do... -

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Basic information

Entry
Database: PDB / ID: 5d3e
TitleCrystal structure of human 14-3-3 gamma in complex with CFTR R-domain peptide pS768-pS795
Components
  • 14-3-3 protein gamma
  • Cystic fibrosis transmembrane conductance regulator
KeywordsSIGNALING PROTEIN / protein-peptide complex / phosphorylation / tandem binding
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 / ATPase-coupled inorganic anion transmembrane transporter activity ...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 / ATPase-coupled inorganic anion transmembrane transporter activity / amelogenesis / chloride channel inhibitor activity / Golgi-associated vesicle membrane / multicellular organismal-level water homeostasis / vesicle docking involved in exocytosis / cholesterol transport / membrane hyperpolarization / bicarbonate transmembrane transporter activity / bicarbonate transport / chloride channel regulator activity / chloride transmembrane transporter activity / sperm capacitation / regulation of neuron differentiation / chloride channel activity / protein kinase C inhibitor activity / cholesterol biosynthetic process / RHOQ GTPase cycle / positive regulation of exocytosis / positive regulation of insulin secretion involved in cellular response to glucose stimulus / chloride channel complex / Regulation of localization of FOXO transcription factors / ATPase-coupled transmembrane transporter activity / phosphoserine residue binding / protein targeting / Activation of BAD and translocation to mitochondria / regulation of signal transduction / cellular response to glucose starvation / ABC-type transporter activity / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / cellular response to forskolin / cellular response to cAMP / RHO GTPases activate PKNs / isomerase activity / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / negative regulation of TORC1 signaling / Recruitment of mitotic centrosome proteins and complexes / chloride transmembrane transport / Recruitment of NuMA to mitotic centrosomes / insulin-like growth factor receptor binding / Anchoring of the basal body to the plasma membrane / response to endoplasmic reticulum stress / AURKA Activation by TPX2 / protein sequestering activity / protein kinase C binding / PDZ domain binding / Translocation of SLC2A4 (GLUT4) to the plasma membrane / establishment of localization in cell / TP53 Regulates Metabolic Genes / Defective CFTR causes cystic fibrosis / clathrin-coated endocytic vesicle membrane / Late endosomal microautophagy / regulation of synaptic plasticity / negative regulation of protein kinase activity / ABC-family proteins mediated transport / transmembrane transport / receptor tyrosine kinase binding / recycling endosome / Aggrephagy / Chaperone Mediated Autophagy / cellular response to insulin stimulus / recycling endosome membrane / Regulation of PLK1 Activity at G2/M Transition / Cargo recognition for clathrin-mediated endocytosis / presynapse / Clathrin-mediated endocytosis / protein-folding chaperone binding / early endosome membrane / early endosome / endosome membrane / Ub-specific processing proteases / apical plasma membrane / lysosomal membrane / protein domain specific binding / focal adhesion / endoplasmic reticulum membrane / enzyme binding / cell surface / signal transduction / ATP hydrolysis activity / protein-containing complex / RNA binding / extracellular exosome / ATP binding / membrane / identical protein binding / nucleus / plasma 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. / 14-3-3 protein ...: / 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
Cystic fibrosis transmembrane conductance regulator / 14-3-3 protein gamma
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 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 1.1Jan 10, 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
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: 14-3-3 protein gamma
B: 14-3-3 protein gamma
C: Cystic fibrosis transmembrane conductance regulator
E: 14-3-3 protein gamma
F: 14-3-3 protein gamma
G: Cystic fibrosis transmembrane conductance regulator
I: 14-3-3 protein gamma
J: 14-3-3 protein gamma
K: Cystic fibrosis transmembrane conductance regulator


Theoretical massNumber of molelcules
Total (without water)180,4339
Polymers180,4339
Non-polymers00
Water2,540141
1
A: 14-3-3 protein gamma
B: 14-3-3 protein gamma
C: Cystic fibrosis transmembrane conductance regulator


Theoretical massNumber of molelcules
Total (without water)60,1443
Polymers60,1443
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: 14-3-3 protein gamma
F: 14-3-3 protein gamma
G: Cystic fibrosis transmembrane conductance regulator


Theoretical massNumber of molelcules
Total (without water)60,1443
Polymers60,1443
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
I: 14-3-3 protein gamma
J: 14-3-3 protein gamma
K: Cystic fibrosis transmembrane conductance regulator


Theoretical massNumber of molelcules
Total (without water)60,1443
Polymers60,1443
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)122.450, 122.450, 313.159
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

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


Mass: 27738.176 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: YWHAG / Production host: Escherichia coli (E. coli) / References: UniProt: P61981
#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: 4668.073 Da / Num. of mol.: 3 / Fragment: UNP residues 762-801 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P13569, EC: 3.6.3.49
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 141 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.09 Å3/Da / Density % sol: 60.23 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: HEPES, NaCl, DTT, (NH4)2SO4, Poly(acrylic acid sodium salt 2100

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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 8, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97886 Å / Relative weight: 1
ReflectionResolution: 2.75→36.3 Å / Num. obs: 62906 / % possible obs: 100 % / Redundancy: 13.6 % / Biso Wilson estimate: 53.42 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.12 / Rpim(I) all: 0.034 / Net I/σ(I): 15.6 / Num. measured all: 856403 / Scaling rejects: 32
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
2.75-2.8212.80.6394.25832045690.8890.186100
12.3-36.313.50.06430.5108898060.9980.01896.3

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
XDSdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4UZD

4uzd


Resolution: 2.75→36.3 Å / FOM work R set: 0.8089 / SU ML: 0.4 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 25.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2436 3058 4.87 %
Rwork0.202 59737 -
obs0.2041 62795 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 174.75 Å2 / Biso mean: 63.19 Å2 / Biso min: 13.16 Å2
Refinement stepCycle: final / Resolution: 2.75→36.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11540 0 10 141 11691
Biso mean--102.58 47.45 -
Num. residues----1430
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01411742
X-RAY DIFFRACTIONf_angle_d1.27115845
X-RAY DIFFRACTIONf_chiral_restr0.0691770
X-RAY DIFFRACTIONf_plane_restr0.0052042
X-RAY DIFFRACTIONf_dihedral_angle_d16.1534493
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 22 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.7501-2.7930.38531270.266626972824
2.793-2.83880.341280.251526502778
2.8388-2.88770.32911380.249626782816
2.8877-2.94020.29531180.249426702788
2.9402-2.99670.34591530.249326582811
2.9967-3.05790.31281350.245926912826
3.0579-3.12430.31111280.235426702798
3.1243-3.1970.27621470.237326782825
3.197-3.27690.27891320.240326752807
3.2769-3.36540.28381280.230126932821
3.3654-3.46430.26031510.227426892840
3.4643-3.57610.25791210.209826962817
3.5761-3.70380.22741280.208727132841
3.7038-3.85190.25951240.190527322856
3.8519-4.0270.23681340.184526992833
4.027-4.2390.20711620.182827032865
4.239-4.50410.22691390.174327182857
4.5041-4.85120.22911480.169827382886
4.8512-5.3380.21491420.18327582900
5.338-6.10720.24551590.211127562915
6.1072-7.68250.22961550.192428122967
7.6825-36.30790.17491610.173729633124

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