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Yorodumi- PDB-7qi1: Crystal structure of human 14-3-3 protein beta in complex with CF... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7qi1 | ||||||
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Title | Crystal structure of human 14-3-3 protein beta in complex with CFTR peptide pS753pS768 and PPI stabilizer CY007424 | ||||||
Components |
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Keywords | PROTEIN TRANSPORT / PPI stabilization / Cystic Fibrosis | ||||||
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 / negative regulation of monoatomic ion transmembrane transport / 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 ...positive regulation of voltage-gated chloride channel activity / positive regulation of cyclic nucleotide-gated ion channel activity / Sec61 translocon complex binding / negative regulation of monoatomic ion transmembrane transport / 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 / membrane hyperpolarization / cholesterol transport / bicarbonate transport / bicarbonate transmembrane transporter activity / chloride channel regulator activity / chloride transmembrane transporter activity / sperm capacitation / small GTPase-mediated signal transduction / chloride channel 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 / Activation of BAD and translocation to mitochondria / protein targeting / 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 cAMP / cellular response to forskolin / RHO GTPases activate PKNs / isomerase activity / chloride transmembrane transport / 14-3-3 protein binding / substantia nigra development / response to endoplasmic reticulum stress / Translocation of SLC2A4 (GLUT4) to the plasma membrane / establishment of localization in cell / PDZ domain binding / TP53 Regulates Metabolic Genes / Defective CFTR causes cystic fibrosis / Late endosomal microautophagy / clathrin-coated endocytic vesicle membrane / ABC-family proteins mediated transport / transmembrane transport / recycling endosome / Aggrephagy / Chaperone Mediated Autophagy / recycling endosome membrane / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / protein-folding chaperone binding / early endosome membrane / transmembrane transporter binding / early endosome / endosome membrane / Ub-specific processing proteases / apical plasma membrane / lysosomal membrane / protein domain specific binding / focal adhesion / negative regulation of DNA-templated transcription / synapse / endoplasmic reticulum membrane / enzyme binding / cell surface / signal transduction / ATP hydrolysis activity / protein-containing complex / extracellular exosome / ATP binding / membrane / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.76 Å | ||||||
Authors | Stevers, L.M. / Ottmann, C. | ||||||
Funding support | Netherlands, 1items
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Citation | Journal: Nat Commun / Year: 2022 Title: Macrocycle-stabilization of its interaction with 14-3-3 increases plasma membrane localization and activity of CFTR. Authors: Stevers, L.M. / Wolter, M. / Carlile, G.W. / Macdonald, D. / Richard, L. / Gielkens, F. / Hanrahan, J.W. / Thomas, D.Y. / Chakka, S.K. / Peterson, M.L. / Thomas, H. / Brunsveld, L. / Ottmann, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7qi1.cif.gz | 220.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7qi1.ent.gz | 172.9 KB | Display | PDB format |
PDBx/mmJSON format | 7qi1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qi/7qi1 ftp://data.pdbj.org/pub/pdb/validation_reports/qi/7qi1 | HTTPS FTP |
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-Related structure data
Related structure data | 6hepS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein / Protein/peptide , 2 types, 6 molecules ABCDFE
#1: Protein | Mass: 27115.580 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: C-terminally truncated 14-3-3 protein beta / Source: (gene. exp.) Homo sapiens (human) / Gene: YWHAQ / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P27348 #2: Protein/peptide | 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 |
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-Non-polymers , 5 types, 547 molecules
#3: Chemical | #4: Chemical | #5: Chemical | #6: Chemical | #7: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 45.67 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop Details: Qiagen Cryos Suite #44 (0.09 M HEPES sodium salt pH7.5, 1.26M tri-sodium citrate, 10% (v/v) glycerol) with an extra 2% (v/v) of glycerol. |
-Data collection
Diffraction | Mean temperature: 293 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.0332 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 1, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 1.76→56.282 Å / Num. obs: 102027 / % possible obs: 99.87 % / Redundancy: 12.9 % / Biso Wilson estimate: 28.91 Å2 / CC1/2: 1 / Net I/σ(I): 20 |
Reflection shell | Resolution: 1.76→1.97 Å / Num. unique obs: 4934 / CC1/2: 0.796 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6HEP Resolution: 1.76→56.28 Å / SU ML: 0.1978 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.4139 Details: A non-canonical order of axes is used in this structure (P2 21 21)
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.9 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.76→56.28 Å
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Refine LS restraints |
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LS refinement shell |
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