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- PDB-8f14: Structure of the STUB1 TPR domain in complex with H201, an all-D ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8f14 | ||||||||||||
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Title | Structure of the STUB1 TPR domain in complex with H201, an all-D Helicon Polypeptide | ||||||||||||
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![]() | LIGASE / E3 ligase / D-peptide / stapled peptide | ||||||||||||
Function / homology | ![]() positive regulation of chaperone-mediated protein complex assembly / regulation of glucocorticoid metabolic process / ubiquitin conjugating enzyme complex / positive regulation of ERAD pathway / positive regulation of mitophagy / ERBB2 signaling pathway / positive regulation of smooth muscle cell apoptotic process / nuclear inclusion body / misfolded protein binding / protein folding chaperone complex ...positive regulation of chaperone-mediated protein complex assembly / regulation of glucocorticoid metabolic process / ubiquitin conjugating enzyme complex / positive regulation of ERAD pathway / positive regulation of mitophagy / ERBB2 signaling pathway / positive regulation of smooth muscle cell apoptotic process / nuclear inclusion body / misfolded protein binding / protein folding chaperone complex / cellular response to misfolded protein / ubiquitin-ubiquitin ligase activity / RIPK1-mediated regulated necrosis / chaperone-mediated autophagy / TPR domain binding / protein quality control for misfolded or incompletely synthesized proteins / SMAD binding / protein monoubiquitination / negative regulation of smooth muscle cell apoptotic process / R-SMAD binding / protein K63-linked ubiquitination / positive regulation of proteolysis / protein maturation / protein autoubiquitination / ERAD pathway / ubiquitin ligase complex / endoplasmic reticulum unfolded protein response / heat shock protein binding / Hsp70 protein binding / Downregulation of TGF-beta receptor signaling / positive regulation of protein ubiquitination / response to ischemia / G protein-coupled receptor binding / Regulation of TNFR1 signaling / negative regulation of transforming growth factor beta receptor signaling pathway / Hsp90 protein binding / RING-type E3 ubiquitin transferase / regulation of protein stability / tau protein binding / Regulation of necroptotic cell death / Downregulation of ERBB2 signaling / kinase binding / Z disc / Regulation of PTEN stability and activity / protein polyubiquitination / ubiquitin-protein transferase activity / Regulation of RUNX2 expression and activity / MAPK cascade / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / protein-macromolecule adaptor activity / cellular response to heat / protein-folding chaperone binding / cellular response to hypoxia / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / protein stabilization / protein ubiquitination / DNA repair / ubiquitin protein ligase binding / enzyme binding / endoplasmic reticulum / protein homodimerization activity / mitochondrion / nucleoplasm / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||||||||
Biological species | ![]() synthetic construct (others) | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Li, K. / Callahan, A.J. / Travaline, T.L. / Tokareva, O.S. / Swiecicki, J.-M. / Verdine, G.L. / Pentelute, B.L. / McGee, J.H. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Single-Shot Flow Synthesis of D-Proteins for Mirror-Image Phage Display Authors: Callahan, A.J. / Gandhesiri, S. / Travaline, T.L. / Lozano Salazar, L / Hanna, S. / Lee, Y.-C. / Li, K. / Tokareva, O.S. / Swiecicki, J.-M. / Loas, A. / Verdine, G.L. / McGee, J.H. / Pentelute, B.L. | ||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 54.2 KB | Display | ![]() |
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PDB format | ![]() | 35.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 467 KB | Display | ![]() |
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Full document | ![]() | 467.7 KB | Display | |
Data in XML | ![]() | 9.3 KB | Display | |
Data in CIF | ![]() | 12.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8f0zC ![]() 8f10C ![]() 8f12C ![]() 8f13C ![]() 8f15C ![]() 8f16C ![]() 8f17C ![]() 3q49S S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
-Protein / Polypeptide(D) , 2 types, 2 molecules AB
#1: Protein | Mass: 15350.439 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q9UNE7, RING-type E3 ubiquitin transferase |
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#2: Polypeptide(D) | Type: Peptide-like / Class: Substrate analog / Mass: 1899.134 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) / References: BIRD: PRD_002512 |
-Non-polymers , 4 types, 139 molecules ![](data/chem/img/SO4.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/WHL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/WHL.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-SO4 / | ||||
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#4: Chemical | #5: Chemical | ChemComp-WHL / | #6: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.78 Å3/Da / Density % sol: 55.81 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 0.2 M Lithium Sulfate, 0.1 M Bis-Tris pH 6.5, 25% w/v PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Dec 11, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.89685 Å / Relative weight: 1 |
Reflection | Resolution: 1.69→92.33 Å / Num. obs: 21997 / % possible obs: 100 % / Redundancy: 13.5 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 20.2 |
Reflection shell | Resolution: 1.69→1.72 Å / Rmerge(I) obs: 1.22 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 1103 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3Q49 Resolution: 1.69→45.06 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.59 / 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: 95.12 Å2 / Biso mean: 34.7675 Å2 / Biso min: 18.47 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.69→45.06 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8
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