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Yorodumi- PDB-6ao5: Crystal structure of human MST2 in complex with SAV1 SARAH domain -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ao5 | ||||||
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Title | Crystal structure of human MST2 in complex with SAV1 SARAH domain | ||||||
Components |
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Keywords | SIGNALING PROTEIN / Hippo / mst autoactivation / dimerization | ||||||
Function / homology | Function and homology information cell differentiation involved in embryonic placenta development / regulation of cell differentiation involved in embryonic placenta development / type II activin receptor binding / primitive hemopoiesis / intestinal epithelial cell differentiation / neural tube formation / positive regulation of extrinsic apoptotic signaling pathway via death domain receptors / regulation of stem cell population maintenance / beta-1 adrenergic receptor binding / negative regulation of cardiac muscle cell proliferation ...cell differentiation involved in embryonic placenta development / regulation of cell differentiation involved in embryonic placenta development / type II activin receptor binding / primitive hemopoiesis / intestinal epithelial cell differentiation / neural tube formation / positive regulation of extrinsic apoptotic signaling pathway via death domain receptors / regulation of stem cell population maintenance / beta-1 adrenergic receptor binding / negative regulation of cardiac muscle cell proliferation / lung epithelial cell differentiation / endocardium development / negative regulation of organ growth / hippo signaling / Signaling by Hippo / protein localization to centrosome / organ growth / ventricular septum morphogenesis / hepatocyte apoptotic process / receptor clustering / SMAD binding / regulation of MAPK cascade / extrinsic apoptotic signaling pathway via death domain receptors / hair follicle development / positive regulation of fat cell differentiation / canonical Wnt signaling pathway / keratinocyte differentiation / JNK cascade / protein serine/threonine kinase activator activity / phosphatidylinositol 3-kinase/protein kinase B signal transduction / epithelial cell proliferation / central nervous system development / protein tetramerization / positive regulation of JNK cascade / negative regulation of canonical Wnt signaling pathway / positive regulation of DNA-binding transcription factor activity / protein import into nucleus / negative regulation of epithelial cell proliferation / cell-cell junction / signaling receptor complex adaptor activity / positive regulation of protein binding / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / protein stabilization / non-specific serine/threonine protein kinase / protein kinase activity / intracellular signal transduction / positive regulation of apoptotic process / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / apoptotic process / dendrite / magnesium ion binding / signal transduction / protein-containing complex / ATP binding / identical protein binding / nucleus / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.955 Å | ||||||
Authors | Tomchick, D.R. / Luo, X. / Ni, L. | ||||||
Citation | Journal: Elife / Year: 2017 Title: SAV1 promotes Hippo kinase activation through antagonizing the PP2A phosphatase STRIPAK. Authors: Bae, S.J. / Ni, L. / Osinski, A. / Tomchick, D.R. / Brautigam, C.A. / Luo, X. #1: Journal: Structure / Year: 2013 Title: Structural basis for autoactivation of human Mst2 kinase and its regulation by RASSF5. Authors: Ni, L. / Li, S. / Yu, J. / Min, J. / Brautigam, C.A. / Tomchick, D.R. / Pan, D. / Luo, X. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ao5.cif.gz | 256.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ao5.ent.gz | 211.4 KB | Display | PDB format |
PDBx/mmJSON format | 6ao5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ao5_validation.pdf.gz | 797.6 KB | Display | wwPDB validaton report |
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Full document | 6ao5_full_validation.pdf.gz | 801.9 KB | Display | |
Data in XML | 6ao5_validation.xml.gz | 16.1 KB | Display | |
Data in CIF | 6ao5_validation.cif.gz | 21.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ao/6ao5 ftp://data.pdbj.org/pub/pdb/validation_reports/ao/6ao5 | HTTPS FTP |
-Related structure data
Related structure data | 6ar0C 6ar2C 4lgdS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 41733.961 Da / Num. of mol.: 1 / Fragment: kinase domain (UNP residues 16-313, 428-491) / Mutation: D146N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: STK3, KRS1, MST2 / Plasmid: PET29 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: Q13188, non-specific serine/threonine protein kinase |
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#2: Protein | Mass: 11270.966 Da / Num. of mol.: 1 / Fragment: SARAH domain (UNP residues 291-383) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SAV1, WW45 / Plasmid: PET29 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9H4B6 |
#3: Chemical | ChemComp-ANP / |
#4: Chemical | ChemComp-MG / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.62 Å3/Da / Density % sol: 65.99 % / Mosaicity: 0.579 ° |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.05 M NaCl, 0.1 M Hepes, 0.19 mM CYMAL-7, 1 mM TCEP, 40% PEG 400 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 12, 2015 / Details: monochromator | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.95→50 Å / Num. obs: 15976 / % possible obs: 99.9 % / Redundancy: 19 % / Biso Wilson estimate: 48.45 Å2 / Rmerge(I) obs: 0.124 / Rpim(I) all: 0.029 / Rrim(I) all: 0.128 / Χ2: 1.085 / Net I/σ(I): 7 / Num. measured all: 303392 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4LGD Resolution: 2.955→42.271 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 28.54 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 192.97 Å2 / Biso mean: 60.0404 Å2 / Biso min: 15.87 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.955→42.271 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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