+Open data
-Basic information
Entry | Database: PDB / ID: 2d5g | ||||||
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Title | Structure of ubiquitin fold protein R767E mutant | ||||||
Components | Axin-1AXIN1 | ||||||
Keywords | SIGNALING PROTEIN / UBIQUITIN FOLD | ||||||
Function / homology | Function and homology information Beta-catenin phosphorylation cascade / Disassembly of the destruction complex and recruitment of AXIN to the membrane / TCF dependent signaling in response to WNT / Degradation of beta-catenin by the destruction complex / Degradation of AXIN / embryonic skeletal joint morphogenesis / armadillo repeat domain binding / hemoglobin metabolic process / response to quercetin / head development ...Beta-catenin phosphorylation cascade / Disassembly of the destruction complex and recruitment of AXIN to the membrane / TCF dependent signaling in response to WNT / Degradation of beta-catenin by the destruction complex / Degradation of AXIN / embryonic skeletal joint morphogenesis / armadillo repeat domain binding / hemoglobin metabolic process / response to quercetin / head development / cell development / Ub-specific processing proteases / dorsal/ventral axis specification / axial mesoderm formation / axial mesoderm development / post-anal tail morphogenesis / epigenetic programming in the zygotic pronuclei / beta-catenin destruction complex / positive regulation of ubiquitin-dependent protein catabolic process / nervous system process / dorsal/ventral pattern formation / I-SMAD binding / negative regulation of protein metabolic process / adult walking behavior / Wnt signalosome / regulation of canonical Wnt signaling pathway / erythrocyte homeostasis / nucleocytoplasmic transport / negative regulation of fat cell differentiation / negative regulation of Wnt signaling pathway / negative regulation of transcription elongation by RNA polymerase II / positive regulation of transforming growth factor beta receptor signaling pathway / SMAD binding / R-SMAD binding / ubiquitin-like ligase-substrate adaptor activity / canonical Wnt signaling pathway / lateral plasma membrane / cytoplasmic microtubule organization / positive regulation of peptidyl-threonine phosphorylation / positive regulation of protein ubiquitination / cell periphery / sensory perception of sound / positive regulation of JNK cascade / regulation of protein phosphorylation / protein catabolic process / negative regulation of canonical Wnt signaling pathway / beta-catenin binding / Wnt signaling pathway / protein polyubiquitination / positive regulation of protein catabolic process / : / microtubule cytoskeleton / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / p53 binding / positive regulation of peptidyl-serine phosphorylation / cell cortex / cytoplasmic vesicle / protein-containing complex assembly / in utero embryonic development / molecular adaptor activity / positive regulation of protein phosphorylation / protein domain specific binding / negative regulation of gene expression / signaling receptor binding / synapse / apoptotic process / ubiquitin protein ligase binding / protein kinase binding / perinuclear region of cytoplasm / enzyme binding / protein homodimerization activity / protein-containing complex / identical protein binding / nucleus / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å | ||||||
Authors | Shibata, N. / Higuchi, Y. | ||||||
Citation | Journal: to be published Title: Structure of ubiquitin fold protein R767E mutant Authors: Shibata, N. / Hanamura, T. / Yamamoto, R. / Ueda, Y. / Yamamoto, H. / Kikuchi, A. / Higuchi, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2d5g.cif.gz | 106.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2d5g.ent.gz | 88.4 KB | Display | PDB format |
PDBx/mmJSON format | 2d5g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d5/2d5g ftp://data.pdbj.org/pub/pdb/validation_reports/d5/2d5g | HTTPS FTP |
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-Related structure data
Related structure data | |
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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: 9803.242 Da / Num. of mol.: 6 / Fragment: DIX DOMAIN / Mutation: R767E Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Plasmid: PMALC2 / Production host: Escherichia coli (E. coli) / Strain (production host): DH5ALPHA / References: UniProt: O70239 #2: Chemical | ChemComp-HG / |
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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: 2.98 Å3/Da / Density % sol: 58.66 % / Description: the file contains Friedel pairs. |
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Crystal grow | Temperature: 283 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: PEG8000, TRIS, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 283K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 19, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→50 Å / Num. all: 21930 / Num. obs: 21930 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 3.2→3.31 Å / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.2→49.18 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 321432.46 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: the file contains Friedel pairs.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 66.6075 Å2 / ksol: 0.281879 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 76.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3.2→49.18 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.2→3.31 Å / Rfactor Rfree error: 0.032 / Total num. of bins used: 10
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Xplor file |
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