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Yorodumi- PDB-6fbk: Crystal structure of the human WNK2 CCT-like 1 domain in complex ... -
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-Basic information
Entry | Database: PDB / ID: 6fbk | ||||||
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Title | Crystal structure of the human WNK2 CCT-like 1 domain in complex with a WNK1 RFXV peptide | ||||||
Components |
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Keywords | PEPTIDE BINDING PROTEIN / WNK2 / CCT Domain / AI domain / RFXV motif binding | ||||||
Function / homology | Function and homology information negative regulation of cell-cell adhesion mediated by integrin / lymphocyte migration into lymph node / chemokine (C-C motif) ligand 21 signaling pathway / positive regulation of termination of RNA polymerase II transcription / monoatomic cation homeostasis / negative regulation of pancreatic juice secretion / protein insertion into ER membrane by stop-transfer membrane-anchor sequence / positive regulation of sodium ion transmembrane transporter activity / positive regulation of mitotic cytokinesis / negative regulation of sodium ion transport ...negative regulation of cell-cell adhesion mediated by integrin / lymphocyte migration into lymph node / chemokine (C-C motif) ligand 21 signaling pathway / positive regulation of termination of RNA polymerase II transcription / monoatomic cation homeostasis / negative regulation of pancreatic juice secretion / protein insertion into ER membrane by stop-transfer membrane-anchor sequence / positive regulation of sodium ion transmembrane transporter activity / positive regulation of mitotic cytokinesis / negative regulation of sodium ion transport / monoatomic ion homeostasis / regulation of mRNA export from nucleus / positive regulation of potassium ion import across plasma membrane / regulation of sodium ion transmembrane transport / intracellular chloride ion homeostasis / negative regulation of heterotypic cell-cell adhesion / positive regulation of T cell chemotaxis / positive regulation of systemic arterial blood pressure / chloride channel inhibitor activity / non-membrane-bounded organelle assembly / potassium ion homeostasis / cellular response to chemokine / potassium channel inhibitor activity / negative regulation of leukocyte cell-cell adhesion / cellular hyperosmotic response / regulation of monoatomic cation transmembrane transport / cell volume homeostasis / negative regulation of protein localization to plasma membrane / negative regulation of GTPase activity / intracellular non-membrane-bounded organelle / protein kinase activator activity / sodium ion transmembrane transport / neuron development / phosphatase binding / monoatomic ion transport / regulation of sodium ion transport / negative regulation of protein ubiquitination / negative regulation of autophagy / molecular condensate scaffold activity / peptidyl-threonine phosphorylation / Stimuli-sensing channels / negative regulation of ERK1 and ERK2 cascade / mitotic spindle / positive regulation of angiogenesis / positive regulation of canonical Wnt signaling pathway / heart development / T cell receptor signaling pathway / peptidyl-serine phosphorylation / protein autophosphorylation / non-specific serine/threonine protein kinase / protein kinase activity / intracellular signal transduction / negative regulation of cell population proliferation / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / protein kinase binding / signal transduction / protein-containing complex / ATP binding / membrane / nucleus / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.743 Å | ||||||
Authors | Pinkas, D.M. / Bufton, J.C. / Burgess-Brown, N.A. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Bullock, A.N. | ||||||
Citation | Journal: To Be Published Title: Crystal structure of the human WNK2 CCT-like 1 domain in complex with a WNK1 RFXV peptide Authors: Pinkas, D.M. / Bufton, J.C. / Burgess-Brown, N.A. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Bullock, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6fbk.cif.gz | 33.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6fbk.ent.gz | 21 KB | Display | PDB format |
PDBx/mmJSON format | 6fbk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6fbk_validation.pdf.gz | 436.8 KB | Display | wwPDB validaton report |
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Full document | 6fbk_full_validation.pdf.gz | 439.6 KB | Display | |
Data in XML | 6fbk_validation.xml.gz | 6.3 KB | Display | |
Data in CIF | 6fbk_validation.cif.gz | 7.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fb/6fbk ftp://data.pdbj.org/pub/pdb/validation_reports/fb/6fbk | HTTPS FTP |
-Related structure data
Related structure data | 6elmS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 11340.844 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: WNK2, KIAA1760, PRKWNK2, SDCCAG43, P/OKcl.13 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta References: UniProt: Q9Y3S1, non-specific serine/threonine protein kinase |
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#2: Protein/peptide | Mass: 2610.046 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) References: UniProt: Q9H4A3, non-specific serine/threonine protein kinase |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.18 Å3/Da / Density % sol: 43.45 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 7.5 Details: 20% PEG3350 -- 10% ethylene glycol -- 0.2M sodium fluoride |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 30, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.74→55.3 Å / Num. obs: 11689 / % possible obs: 99.3 % / Redundancy: 6.5 % / Net I/σ(I): 20.7 |
Reflection shell | Resolution: 1.743→1.773 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6ELM Resolution: 1.743→33.973 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 50.6 Details: Refinement R factors are higher than expected for resolution and diffraction images show diffuse spots between the indexed spots that were not able to be integrated. Nevertheless, the structure appears correct.
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.743→33.973 Å
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Refine LS restraints |
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LS refinement shell |
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