+Open data
-Basic information
Entry | Database: PDB / ID: 4zri | ||||||
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Title | Crystal structure of Merlin-FERM and Lats2 | ||||||
Components |
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Keywords | SIGNALING PROTEIN/TRANSFERASE / Merlin / FERM / Lats2 / SIGNALING PROTEIN-TRANSFERASE complex | ||||||
Function / homology | Function and homology information regulation of hippo signaling / regulation of organelle assembly / regulation of gliogenesis / positive regulation of early endosome to late endosome transport / Schwann cell proliferation / osteoblast proliferation / negative regulation of tyrosine phosphorylation of STAT protein / negative regulation of Schwann cell proliferation / negative regulation of osteoblast proliferation / positive regulation of protein localization to early endosome ...regulation of hippo signaling / regulation of organelle assembly / regulation of gliogenesis / positive regulation of early endosome to late endosome transport / Schwann cell proliferation / osteoblast proliferation / negative regulation of tyrosine phosphorylation of STAT protein / negative regulation of Schwann cell proliferation / negative regulation of osteoblast proliferation / positive regulation of protein localization to early endosome / ectoderm development / lens fiber cell differentiation / regulation of neural precursor cell proliferation / hippo signaling / regulation of stem cell proliferation / negative regulation of receptor signaling pathway via JAK-STAT / negative regulation of cyclin-dependent protein serine/threonine kinase activity / cell-cell junction organization / regulation of organ growth / regulation of protein localization to nucleus / filopodium membrane / Signaling by Hippo / negative regulation of MAPK cascade / cortical actin cytoskeleton / negative regulation of cell-matrix adhesion / negative regulation of cell-cell adhesion / RHO GTPases activate PAKs / odontogenesis of dentin-containing tooth / cleavage furrow / mesoderm formation / centriolar satellite / positive regulation of stress fiber assembly / hormone-mediated signaling pathway / negative regulation of cell migration / filopodium / hippocampus development / positive regulation of cell differentiation / adherens junction / regulation of protein stability / negative regulation of canonical Wnt signaling pathway / G1/S transition of mitotic cell cycle / Regulation of actin dynamics for phagocytic cup formation / ruffle membrane / spindle pole / MAPK cascade / integrin binding / apical part of cell / lamellipodium / actin binding / cell body / regulation of cell shape / actin cytoskeleton organization / peptidyl-serine phosphorylation / regulation of apoptotic process / early endosome / cytoskeleton / non-specific serine/threonine protein kinase / regulation of cell cycle / intracellular signal transduction / neuron projection / positive regulation of apoptotic process / negative regulation of cell population proliferation / cell division / protein phosphorylation / protein serine/threonine kinase activity / nucleolus / perinuclear region of cytoplasm / ATP binding / membrane / metal ion binding / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Li, F. / Zhou, H. / Long, J. / Shen, Y. | ||||||
Citation | Journal: Cell Res. / Year: 2015 Title: Angiomotin binding-induced activation of Merlin/NF2 in the Hippo pathway Authors: Li, Y. / Zhou, H. / Li, F. / Chan, S.W. / Lin, Z. / Wei, Z. / Yang, Z. / Guo, F. / Lim, C.J. / Xing, W. / Shen, Y. / Hong, W. / Long, J. / Zhang, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4zri.cif.gz | 255.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4zri.ent.gz | 205.8 KB | Display | PDB format |
PDBx/mmJSON format | 4zri.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zr/4zri ftp://data.pdbj.org/pub/pdb/validation_reports/zr/4zri | HTTPS FTP |
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-Related structure data
Related structure data | 4zrjC 4zrkC 1isnS C: citing same article (ref.) 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 38028.914 Da / Num. of mol.: 2 / Fragment: FERM domain, UNP residues 1-320 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: NF2, SCH / Production host: Escherichia coli (E. coli) / References: UniProt: P35240 #2: Protein/peptide | Mass: 3515.967 Da / Num. of mol.: 2 / Fragment: UNP residues 68-99 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: LATS2, KPM / Production host: Escherichia coli (E. coli) / References: UniProt: Q9NRM7 #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.38 Å3/Da / Density % sol: 48.39 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 18% iso-Propanol, 0.1M Tris, 5% PEG8000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9791 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 23, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→50 Å / Num. obs: 21376 / % possible obs: 99.3 % / Redundancy: 3.8 % / Net I/σ(I): 20.4 |
Reflection shell | Resolution: 2.7→2.79 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.406 / Mean I/σ(I) obs: 2.2 / % possible all: 95 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1ISN Resolution: 2.7→36.008 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 31.62 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→36.008 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 44.1048 Å / Origin y: -6.2063 Å / Origin z: 121.3127 Å
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Refinement TLS group | Selection details: all |