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Open data
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Basic information
Entry | Database: PDB / ID: 7t1y | ||||||
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Title | Structure of the Fbw7-Skp1-MycCdegron complex | ||||||
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![]() | LIGASE / Ubiquitin ligase / WD40 | ||||||
Function / homology | ![]() negative regulation of SREBP signaling pathway / negative regulation of triglyceride biosynthetic process / negative regulation of hepatocyte proliferation / regulation of lipid storage / Parkin-FBXW7-Cul1 ubiquitin ligase complex / ubiquitin recycling / ubiquitin-protein transferase activator activity / F-box domain binding / regulation of mitophagy / phosphothreonine residue binding ...negative regulation of SREBP signaling pathway / negative regulation of triglyceride biosynthetic process / negative regulation of hepatocyte proliferation / regulation of lipid storage / Parkin-FBXW7-Cul1 ubiquitin ligase complex / ubiquitin recycling / ubiquitin-protein transferase activator activity / F-box domain binding / regulation of mitophagy / phosphothreonine residue binding / regulation of cell cycle G1/S phase transition / negative regulation of osteoclast development / PcG protein complex / positive regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / positive regulation of ubiquitin protein ligase activity / Cul7-RING ubiquitin ligase complex / maintenance of protein location in nucleus / Loss of Function of FBXW7 in Cancer and NOTCH1 Signaling / positive regulation of proteasomal protein catabolic process / vasculature development / positive regulation of ubiquitin-dependent protein catabolic process / positive regulation of protein targeting to mitochondrion / sister chromatid cohesion / SCF ubiquitin ligase complex / positive regulation of epidermal growth factor receptor signaling pathway / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / ubiquitin ligase complex scaffold activity / Prolactin receptor signaling / lipid homeostasis / Association of TriC/CCT with target proteins during biosynthesis / cullin family protein binding / negative regulation of Notch signaling pathway / protein monoubiquitination / ubiquitin-like ligase-substrate adaptor activity / protein K48-linked ubiquitination / Nuclear events stimulated by ALK signaling in cancer / cyclin binding / Regulation of BACH1 activity / MAP3K8 (TPL2)-dependent MAPK1/3 activation / molecular function activator activity / ubiquitin binding / positive regulation of protein ubiquitination / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / Vpu mediated degradation of CD4 / Dectin-1 mediated noncanonical NF-kB signaling / Activation of NF-kappaB in B cells / Degradation of GLI1 by the proteasome / Iron uptake and transport / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / Negative regulation of NOTCH4 signaling / Degradation of GLI2 by the proteasome / GLI3 is processed to GLI3R by the proteasome / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / regulation of circadian rhythm / beta-catenin binding / Degradation of beta-catenin by the destruction complex / NOTCH1 Intracellular Domain Regulates Transcription / CLEC7A (Dectin-1) signaling / SCF(Skp2)-mediated degradation of p27/p21 / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / FCERI mediated NF-kB activation / Interleukin-1 signaling / Orc1 removal from chromatin / protein polyubiquitination / Regulation of RUNX2 expression and activity / Cyclin D associated events in G1 / cellular response to UV / rhythmic process / : / Regulation of PLK1 Activity at G2/M Transition / Antigen processing: Ubiquitination & Proteasome degradation / Downstream TCR signaling / regulation of protein localization / chromosome / Neddylation / protein-macromolecule adaptor activity / proteasome-mediated ubiquitin-dependent protein catabolic process / positive regulation of ERK1 and ERK2 cascade / protein stabilization / protein ubiquitination / chromatin remodeling / protein domain specific binding / negative regulation of gene expression / DNA repair / centrosome / ubiquitin protein ligase binding / DNA damage response / nucleolus / protein-containing complex / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Wang, B. / Rusnac, D.V. / Clurman, B.E. / Zheng, N. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Two diphosphorylated degrons control c-Myc degradation by the Fbw7 tumor suppressor. Authors: Welcker, M. / Wang, B. / Rusnac, D.V. / Hussaini, Y. / Swanger, J. / Zheng, N. / Clurman, B.E. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 143 KB | Display | ![]() |
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PDB format | ![]() | 100.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 468.8 KB | Display | ![]() |
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Full document | ![]() | 485.2 KB | Display | |
Data in XML | ![]() | 24.3 KB | Display | |
Data in CIF | ![]() | 33.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7t1zC ![]() 2ovpS 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: 17936.336 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||||
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#2: Protein | Mass: 51584.789 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||||
#3: Protein/peptide | Mass: 3541.408 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() | ||||||
#4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | Has protein modification | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 5.27 Å3/Da / Density % sol: 76.66 % |
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Crystal grow | Temperature: 298.15 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.1 M Bicine pH6.5, 1.6 M Li2SO4 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 29, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.55→50 Å / Num. obs: 48054 / % possible obs: 99.7 % / Redundancy: 9.5 % / Biso Wilson estimate: 50.87 Å2 / CC1/2: 0.995 / Net I/σ(I): 19.11 |
Reflection shell | Resolution: 2.55→2.59 Å / Redundancy: 6.2 % / Num. unique obs: 2297 / CC1/2: 0.676 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2ovp Resolution: 2.55→49.98 Å / SU ML: 0.4176 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 30.6435 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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 mean: 60.65 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.55→49.98 Å
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Refine LS restraints |
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LS refinement shell |
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