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Open data
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Basic information
Entry | Database: PDB / ID: 6le6 | ||||||
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Title | Structure of LNLPTQGRAR bound FEM1C | ||||||
![]() | Protein fem-1 homolog C,10-mer peptide | ||||||
![]() | PROTEIN BINDING / ubiquitination E3 ligase | ||||||
Function / homology | ![]() ubiquitin-dependent protein catabolic process via the C-end degron rule pathway / negative regulation of non-canonical NF-kappaB signal transduction / Cul2-RING ubiquitin ligase complex / ubiquitin-like ligase-substrate adaptor activity / ubiquitin ligase complex / Neddylation / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / protein ubiquitination / nucleoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Chen, X. / Liao, S. / Xu, C. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Molecular basis for arginine C-terminal degron recognition by Cul2 FEM1 E3 ligase. Authors: Chen, X. / Liao, S. / Makaros, Y. / Guo, Q. / Zhu, Z. / Krizelman, R. / Dahan, K. / Tu, X. / Yao, X. / Koren, I. / Xu, C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 301.4 KB | Display | ![]() |
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PDB format | ![]() | 243.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 457.2 KB | Display | ![]() |
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Full document | ![]() | 462.9 KB | Display | |
Data in XML | ![]() | 27.9 KB | Display | |
Data in CIF | ![]() | 38.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6lbfSC ![]() 6lbgC ![]() 6lbnC ![]() 6ldpC ![]() 6lenC ![]() 6leyC ![]() 6lf0C ![]() 7cngC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 45524.996 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: FEM1C fused with a 10-mer peptide LNLPTQGRAR, linked with linker residues GGGSGGGSGGGSGGGS. Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.76 Å3/Da / Density % sol: 67.31 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.6M Lithium sulfate, 0.1M BIS-TRIS propane Ph 6.4 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 17, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.33→94.52 Å / Num. obs: 57097 / % possible obs: 99.3 % / Redundancy: 13.4 % / CC1/2: 0.999 / Net I/σ(I): 17.9 |
Reflection shell | Resolution: 2.33→2.39 Å / Num. unique obs: 5517 / CC1/2: 0.931 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6LBF Resolution: 2.33→79.421 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 31.47
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 176.89 Å2 / Biso mean: 71.357 Å2 / Biso min: 33.53 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.33→79.421 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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