+Open data
-Basic information
Entry | Database: PDB / ID: 8heo | ||||||
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Title | Crystal structure of SIAH1 SBD bound to Axin2 peptide | ||||||
Components |
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Keywords | LIGASE / E3 ubiquitin ligase / SIAH1 / Axin2 / Wnt pathway | ||||||
Function / homology | Function and homology information regulation of mismatch repair / regulation of chondrocyte development / : / chondrocyte differentiation involved in endochondral bone morphogenesis / secondary heart field specification / maintenance of DNA repeat elements / Binding of TCF/LEF:CTNNB1 to target gene promoters / osteoblast proliferation / regulation of centromeric sister chromatid cohesion / cell development ...regulation of mismatch repair / regulation of chondrocyte development / : / chondrocyte differentiation involved in endochondral bone morphogenesis / secondary heart field specification / maintenance of DNA repeat elements / Binding of TCF/LEF:CTNNB1 to target gene promoters / osteoblast proliferation / regulation of centromeric sister chromatid cohesion / cell development / Netrin-1 signaling / mitral valve morphogenesis / intramembranous ossification / negative regulation of osteoblast proliferation / regulation of extracellular matrix organization / beta-catenin destruction complex / mRNA stabilization / I-SMAD binding / aortic valve morphogenesis / ubiquitin conjugating enzyme binding / odontogenesis / bone mineralization / anatomical structure morphogenesis / canonical Wnt signaling pathway / positive regulation of fat cell differentiation / negative regulation of osteoblast differentiation / somitogenesis / positive regulation of epithelial to mesenchymal transition / positive regulation of intrinsic apoptotic signaling pathway / cellular response to dexamethasone stimulus / TCF dependent signaling in response to WNT / stem cell proliferation / Degradation of AXIN / axon guidance / RING-type E3 ubiquitin transferase / protein catabolic process / negative regulation of canonical Wnt signaling pathway / protein localization / beta-catenin binding / Wnt signaling pathway / osteoblast differentiation / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Antigen processing: Ubiquitination & Proteasome degradation / nervous system development / ubiquitin-dependent protein catabolic process / spermatogenesis / proteasome-mediated ubiquitin-dependent protein catabolic process / neuron apoptotic process / amyloid fibril formation / molecular adaptor activity / protein ubiquitination / Ub-specific processing proteases / positive regulation of protein phosphorylation / positive regulation of apoptotic process / cell cycle / Amyloid fiber formation / centrosome / apoptotic process / ubiquitin protein ligase binding / protein kinase binding / enzyme binding / zinc ion binding / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.53 Å | ||||||
Authors | Yan, X.X. / Tian, L.F. | ||||||
Funding support | 1items
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Citation | Journal: To Be Published Title: Crystal structure of SIAH1 SBD bound to Axin2 peptide Authors: Yan, X.X. / Tian, L.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8heo.cif.gz | 90 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8heo.ent.gz | 66.6 KB | Display | PDB format |
PDBx/mmJSON format | 8heo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/he/8heo ftp://data.pdbj.org/pub/pdb/validation_reports/he/8heo | HTTPS FTP |
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-Related structure data
Related structure data | 5wzzS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-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: 21822.998 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SIAH1, HUMSIAH / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: Q8IUQ4, RING-type E3 ubiquitin transferase #2: Protein/peptide | | Mass: 2340.714 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: AXIN2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9Y2T1 #3: Chemical | ChemComp-ZN / #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.28 Å3/Da / Density % sol: 46.11 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / Details: 0.1M Bis-tris propane pH 8.0, 24% PEG 6000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97929 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 12, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97929 Å / Relative weight: 1 |
Reflection | Resolution: 2.53→29.58 Å / Num. obs: 13846 / % possible obs: 99.9 % / Redundancy: 6.7 % / Rpim(I) all: 0.046 / Net I/σ(I): 2.22 |
Reflection shell | Resolution: 2.53→2.59 Å / Num. unique obs: 943 / CC1/2: 0.953 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5WZZ Resolution: 2.53→29.2 Å / Cross valid method: FREE R-VALUE
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Refinement step | Cycle: LAST / Resolution: 2.53→29.2 Å
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