+Open data
-Basic information
Entry | Database: PDB / ID: 3wa0 | ||||||
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Title | Crystal structure of merlin complexed with DCAF1/VprBP | ||||||
Components |
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Keywords | CELL ADHESION / merlin FERM domain | ||||||
Function / homology | Function and homology information regulation of hippo signaling / RHO GTPases activate PAKs / histone H2AT120 kinase activity / regulation of organelle assembly / cell competition in a multicellular organism / regulation of gliogenesis / positive regulation of early endosome to late endosome transport / Schwann cell proliferation / osteoblast proliferation / negative regulation of Schwann cell proliferation ...regulation of hippo signaling / RHO GTPases activate PAKs / histone H2AT120 kinase activity / regulation of organelle assembly / cell competition in a multicellular organism / regulation of gliogenesis / positive regulation of early endosome to late endosome transport / Schwann cell proliferation / osteoblast proliferation / negative regulation of Schwann cell proliferation / negative regulation of osteoblast proliferation / negative regulation of tyrosine phosphorylation of STAT protein / Regulation of actin dynamics for phagocytic cup formation / ectoderm development / lens fiber cell differentiation / positive regulation of protein localization to early endosome / regulation of neural precursor cell proliferation / regulation of stem cell proliferation / negative regulation of receptor signaling pathway via JAK-STAT / cell-cell junction organization / V(D)J recombination / Cul4-RING E3 ubiquitin ligase complex / regulation of protein localization to nucleus / cortical actin cytoskeleton / negative regulation of MAPK cascade / negative regulation of cell-cell adhesion / odontogenesis of dentin-containing tooth / cleavage furrow / ubiquitin-like ligase-substrate adaptor activity / mesoderm formation / regulation of neurogenesis / positive regulation of stress fiber assembly / ruffle / post-translational protein modification / B cell differentiation / filopodium / nuclear estrogen receptor binding / hippocampus development / positive regulation of cell differentiation / adherens junction / brain development / regulation of protein stability / negative regulation of cell growth / fibrillar center / beta-catenin binding / positive regulation of protein catabolic process / MAPK cascade / Antigen processing: Ubiquitination & Proteasome degradation / integrin binding / apical part of cell / lamellipodium / cell body / actin binding / regulation of cell population proliferation / regulation of cell shape / actin cytoskeleton organization / regulation of apoptotic process / protein ubiquitination / cytoskeleton / early endosome / regulation of cell cycle / non-specific serine/threonine protein kinase / neuron projection / protein domain specific binding / negative regulation of cell population proliferation / phosphorylation / protein serine kinase activity / nucleolus / perinuclear region of cytoplasm / negative regulation of transcription by RNA polymerase II / protein-containing complex / nucleoplasm / ATP binding / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.31 Å | ||||||
Authors | Mori, T. / Gotoh, S. / Shirakawa, M. / Hakoshima, T. | ||||||
Citation | Journal: Genes Cells / Year: 2014 Title: Structural basis of DDB1-and-Cullin 4-associated Factor 1 (DCAF1) recognition by merlin/NF2 and its implication in tumorigenesis by CD44-mediated inhibition of merlin suppression of DCAF1 function. Authors: Mori, T. / Gotoh, S. / Shirakawa, M. / Hakoshima, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3wa0.cif.gz | 380.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3wa0.ent.gz | 311.5 KB | Display | PDB format |
PDBx/mmJSON format | 3wa0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wa/3wa0 ftp://data.pdbj.org/pub/pdb/validation_reports/wa/3wa0 | HTTPS FTP |
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-Related structure data
Related structure data | 1isnS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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6 |
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Unit cell |
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-Components
-Protein , 2 types, 8 molecules ABCDEFGH
#1: Protein | Mass: 35517.992 Da / Num. of mol.: 6 / Fragment: UNP residues 19-314 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Strain: DH5a / Gene: Nf2 / Plasmid: pGEX-6P3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21Star(DE3) / References: UniProt: P46662 #2: Protein | Mass: 10486.212 Da / Num. of mol.: 2 / Fragment: UNP residues 1417-1506 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Strain: DH5a / Gene: DCAF1 / Plasmid: pGEX-6P3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21Star(DE3) / References: UniProt: Q9Y4B6 |
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-Protein/peptide , 3 types, 3 molecules IJK
#3: Protein/peptide | Mass: 613.749 Da / Num. of mol.: 1 / Fragment: UNP residues 1417-1506 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Strain: DH5a / Gene: DCAF1 / Plasmid: pGEX-6P3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21Star(DE3) |
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#4: Protein/peptide | Mass: 698.854 Da / Num. of mol.: 1 / Fragment: UNP residues 1417-1506 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Strain: DH5a / Gene: DCAF1 / Plasmid: pGEX-6P3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21Star(DE3) |
#5: Protein/peptide | Mass: 528.644 Da / Num. of mol.: 1 / Fragment: UNP residues 1417-1506 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Strain: DH5a / Gene: DCAF1 / Plasmid: pGEX-6P3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21Star(DE3) |
-Non-polymers , 1 types, 543 molecules
#6: Water | ChemComp-HOH / |
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-Details
Sequence details | SEQUENCE OF CHAIN G,H,I,J,K CORRESPONDS TO ISOFORM 2, Q9Y4B6-2. THE DEPOSITORS BELIEVE THAT CHAIN ...SEQUENCE OF CHAIN G,H,I,J,K CORRESPOND |
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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: 2.93 Å3/Da / Density % sol: 58 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.8 Details: 0.2M ammonium fluoride, 23% PEG 3350, pH 6.8, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å |
Detector | Date: Jun 21, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→20.07 Å / Num. obs: 120906 / % possible obs: 99.7 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1ISN Resolution: 2.31→20.07 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.924 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / ESU R: 0.299 / ESU R Free: 0.228 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 143.79 Å2 / Biso mean: 60.9055 Å2 / Biso min: 21.6 Å2
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Refinement step | Cycle: LAST / Resolution: 2.31→20.07 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.31→2.369 Å / Total num. of bins used: 20
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