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- PDB-6hep: Crystal structure of human 14-3-3 beta in complex with CFTR R-dom... -

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Basic information

Entry
Database: PDB / ID: 6hep
TitleCrystal structure of human 14-3-3 beta in complex with CFTR R-domain peptide pS753-pS768
Components
  • 14-3-3 protein beta/alpha
  • Cystic fibrosis transmembrane conductance regulator
KeywordsSIGNALING PROTEIN / 14-3-3 / CFTR / multivalency
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 / Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / 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 / Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / amelogenesis / Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA / intracellular pH elevation / chloride channel inhibitor activity / : / MTOR signalling / Golgi-associated vesicle membrane / multicellular organismal-level water homeostasis / ARMS-mediated activation / cholesterol transport / SHOC2 M1731 mutant abolishes MRAS complex function / Gain-of-function MRAS complexes activate RAF signaling / bicarbonate transport / Rap1 signalling / bicarbonate transmembrane transporter activity / Signaling by Hippo / vesicle docking involved in exocytosis / chloride channel regulator activity / membrane hyperpolarization / chloride transmembrane transporter activity / vacuolar membrane / negative regulation of G protein-coupled receptor signaling pathway / negative regulation of protein import into nucleus / protein phosphatase inhibitor activity / Frs2-mediated activation / cholesterol biosynthetic process / sperm capacitation / protein kinase inhibitor activity / RHOQ GTPase cycle / chloride channel activity / mTORC1-mediated signalling / positive regulation of exocytosis / Regulation of localization of FOXO transcription factors / ATPase-coupled transmembrane transporter activity / phosphoserine residue binding / 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 / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / RHO GTPases activate PKNs / 14-3-3 protein binding / transcription repressor complex / Transcriptional and post-translational regulation of MITF-M expression and activity / cellular response to forskolin / protein sequestering activity / response to endoplasmic reticulum stress / chloride transmembrane transport / cellular response to cAMP / Defective CFTR causes cystic fibrosis / Late endosomal microautophagy / Translocation of SLC2A4 (GLUT4) to the plasma membrane / TP53 Regulates Metabolic Genes / PDZ domain binding / phosphoprotein binding / ABC-family proteins mediated transport / establishment of localization in cell / clathrin-coated endocytic vesicle membrane / RAF activation / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / recycling endosome / Chaperone Mediated Autophagy / Aggrephagy / Negative regulation of MAPK pathway / transmembrane transport / histone deacetylase binding / recycling endosome membrane / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / Cargo recognition for clathrin-mediated endocytosis / Signaling by BRAF and RAF1 fusions / Clathrin-mediated endocytosis / melanosome / intracellular protein localization / protein-folding chaperone binding / early endosome membrane / early endosome / endosome membrane / Ub-specific processing proteases / apical plasma membrane / cadherin binding / protein domain specific binding / lysosomal membrane / focal adhesion / negative regulation of DNA-templated transcription
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
Chem-ETE / Cystic fibrosis transmembrane conductance regulator / 14-3-3 protein beta/alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.86 Å
AuthorsStevers, L.M. / Ottmann, C. / Brunsveld, L.
Funding support Netherlands, 3items
OrganizationGrant numberCountry
Netherlands Organisation for Scientific Research024.001.035 Netherlands
Netherlands Organisation for Scientific Research2012 022.004.027 Netherlands
Netherlands Organisation for Scientific Research016.150.366 Netherlands
CitationJournal: J. Am. Chem. Soc. / Year: 2018
Title: A Thermodynamic Model for Multivalency in 14-3-3 Protein-Protein Interactions.
Authors: Stevers, L.M. / de Vink, P.J. / Ottmann, C. / Huskens, J. / Brunsveld, L.
History
DepositionAug 20, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 24, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 7, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Nov 13, 2024Group: 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
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 beta/alpha
B: 14-3-3 protein beta/alpha
C: 14-3-3 protein beta/alpha
D: 14-3-3 protein beta/alpha
E: Cystic fibrosis transmembrane conductance regulator
F: Cystic fibrosis transmembrane conductance regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,8808
Polymers114,4636
Non-polymers4172
Water13,241735
1
A: 14-3-3 protein beta/alpha
B: 14-3-3 protein beta/alpha
E: Cystic fibrosis transmembrane conductance regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,4404
Polymers57,2323
Non-polymers2081
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5170 Å2
ΔGint-31 kcal/mol
Surface area23340 Å2
MethodPISA
2
C: 14-3-3 protein beta/alpha
D: 14-3-3 protein beta/alpha
F: Cystic fibrosis transmembrane conductance regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,4404
Polymers57,2323
Non-polymers2081
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4910 Å2
ΔGint-32 kcal/mol
Surface area22280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.619, 111.599, 130.750
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
14-3-3 protein beta/alpha / Protein 1054 / Protein kinase C inhibitor protein 1 / KCIP-1


Mass: 26987.451 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: YWHAB / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P31946
#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.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P13569, EC: 3.6.3.49
#3: Chemical ChemComp-ETE / 2-{2-[2-2-(METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL


Mass: 208.252 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H20O5
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 735 / Source method: isolated from a natural source / Formula: H2O
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: 2.25 Å3/Da / Density % sol: 45.35 %
Crystal growTemperature: 278 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 0.1M Tris, 25% v/v PEG350 MME

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.07027 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Nov 26, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07027 Å / Relative weight: 1
ReflectionResolution: 1.34→70.62 Å / Num. obs: 231938 / % possible obs: 99.7 % / Redundancy: 12.3 % / Net I/σ(I): 6.7
Reflection shellResolution: 1.68→10 Å

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Processing

Software
NameVersionClassification
PHENIX(dev_3139: ???)refinement
MOSFLMdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementResolution: 1.86→65.375 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.57
RfactorNum. reflection% reflection
Rfree0.251 4375 5.04 %
Rwork0.201 --
obs0.2035 86831 99.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.86→65.375 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7585 0 28 735 8348
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0077743
X-RAY DIFFRACTIONf_angle_d0.7910421
X-RAY DIFFRACTIONf_dihedral_angle_d6.1326229
X-RAY DIFFRACTIONf_chiral_restr0.0441163
X-RAY DIFFRACTIONf_plane_restr0.0041339
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.86-1.88110.31151260.28682662X-RAY DIFFRACTION99
1.8811-1.90330.39451380.28822730X-RAY DIFFRACTION99
1.9033-1.92650.32021230.28342715X-RAY DIFFRACTION99
1.9265-1.95090.27441570.27012737X-RAY DIFFRACTION100
1.9509-1.97650.3641470.26272724X-RAY DIFFRACTION100
1.9765-2.00360.31141460.24022749X-RAY DIFFRACTION100
2.0036-2.03230.30271480.23562688X-RAY DIFFRACTION100
2.0323-2.06260.26961400.22372752X-RAY DIFFRACTION99
2.0626-2.09480.27121400.21962694X-RAY DIFFRACTION99
2.0948-2.12920.25511440.21652658X-RAY DIFFRACTION97
2.1292-2.16590.26691540.21782654X-RAY DIFFRACTION97
2.1659-2.20530.25881430.21162742X-RAY DIFFRACTION100
2.2053-2.24770.231460.20882716X-RAY DIFFRACTION100
2.2477-2.29360.27311700.19882753X-RAY DIFFRACTION100
2.2936-2.34340.26611470.19572724X-RAY DIFFRACTION100
2.3434-2.3980.22961470.18872737X-RAY DIFFRACTION100
2.398-2.45790.21641440.18892749X-RAY DIFFRACTION100
2.4579-2.52440.2731430.19042782X-RAY DIFFRACTION100
2.5244-2.59870.27841390.19472746X-RAY DIFFRACTION100
2.5987-2.68260.23521420.20172748X-RAY DIFFRACTION100
2.6826-2.77840.27151820.19732729X-RAY DIFFRACTION100
2.7784-2.88970.26271480.20182738X-RAY DIFFRACTION100
2.8897-3.02120.24011360.20352759X-RAY DIFFRACTION98
3.0212-3.18050.2451500.20122757X-RAY DIFFRACTION99
3.1805-3.37970.22981340.18822824X-RAY DIFFRACTION100
3.3797-3.64070.23011300.19192786X-RAY DIFFRACTION100
3.6407-4.0070.22211440.17862809X-RAY DIFFRACTION100
4.007-4.58670.23131500.16752791X-RAY DIFFRACTION99
4.5867-5.77820.24311420.19072851X-RAY DIFFRACTION99
5.7782-100.22591750.19452952X-RAY DIFFRACTION99

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