+Open data
-Basic information
Entry | Database: PDB / ID: 7t1z | ||||||
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Title | Structure of the Fbw7-Skp1-MycNdegron complex | ||||||
Components |
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Keywords | LIGASE / Ubiquitin ligase / WD40 | ||||||
Function / homology | Function and homology information negative regulation of SREBP signaling pathway / negative regulation of triglyceride biosynthetic process / regulation of cell migration involved in sprouting angiogenesis / negative regulation of hepatocyte proliferation / regulation of lipid storage / positive regulation of epidermal growth factor-activated receptor activity / Parkin-FBXW7-Cul1 ubiquitin ligase complex / F-box domain binding / ubiquitin recycling / ubiquitin-protein transferase activator activity ...negative regulation of SREBP signaling pathway / negative regulation of triglyceride biosynthetic process / regulation of cell migration involved in sprouting angiogenesis / negative regulation of hepatocyte proliferation / regulation of lipid storage / positive regulation of epidermal growth factor-activated receptor activity / Parkin-FBXW7-Cul1 ubiquitin ligase complex / F-box domain binding / ubiquitin recycling / ubiquitin-protein transferase activator activity / regulation of mitophagy / PcG protein complex / phosphothreonine residue binding / regulation of cell cycle G1/S phase transition / negative regulation of osteoclast development / positive regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / positive regulation of proteasomal protein catabolic process / Cul7-RING ubiquitin ligase complex / positive regulation of ubiquitin protein ligase activity / maintenance of protein location in nucleus / positive regulation of ubiquitin-dependent protein catabolic process / Loss of Function of FBXW7 in Cancer and NOTCH1 Signaling / vasculature development / sister chromatid cohesion / positive regulation of ubiquitin-protein transferase activity / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / positive regulation of protein targeting to mitochondrion / SCF ubiquitin ligase complex / ubiquitin ligase complex scaffold activity / negative regulation of Notch signaling pathway / Prolactin receptor signaling / protein monoubiquitination / Association of TriC/CCT with target proteins during biosynthesis / lipid homeostasis / cullin family protein binding / ubiquitin-like ligase-substrate adaptor activity / protein K48-linked ubiquitination / vasculogenesis / Nuclear events stimulated by ALK signaling in cancer / Notch signaling pathway / Regulation of BACH1 activity / cyclin binding / MAP3K8 (TPL2)-dependent MAPK1/3 activation / ubiquitin binding / positive regulation of protein ubiquitination / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / molecular function activator activity / Vpu mediated degradation of CD4 / Dectin-1 mediated noncanonical NF-kB signaling / Degradation of GLI1 by the proteasome / Activation of NF-kappaB in B cells / Negative regulation of NOTCH4 signaling / Iron uptake and transport / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / lung development / 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 / protein destabilization / Degradation of beta-catenin by the destruction complex / regulation of circadian rhythm / NOTCH1 Intracellular Domain Regulates Transcription / CLEC7A (Dectin-1) signaling / SCF(Skp2)-mediated degradation of p27/p21 / beta-catenin binding / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / FCERI mediated NF-kB activation / Interleukin-1 signaling / protein polyubiquitination / Orc1 removal from chromatin / Regulation of RUNX2 expression and activity / cellular response to UV / Cyclin D associated events in G1 / rhythmic process / regulation of protein localization / Regulation of PLK1 Activity at G2/M Transition / protein-macromolecule adaptor activity / Antigen processing: Ubiquitination & Proteasome degradation / Circadian Clock / Downstream TCR signaling / Neddylation / chromosome / 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 / DNA damage response / ubiquitin protein ligase binding / nucleolus / perinuclear region of cytoplasm / Golgi apparatus / endoplasmic reticulum / protein-containing complex Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.77 Å | ||||||
Authors | Wang, B. / Rusnac, D.V. / Clurman, B.E. / Zheng, N. | ||||||
Funding support | United States, 1items
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Citation | Journal: Sci Adv / Year: 2022 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7t1z.cif.gz | 143.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7t1z.ent.gz | 100.7 KB | Display | PDB format |
PDBx/mmJSON format | 7t1z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t1/7t1z ftp://data.pdbj.org/pub/pdb/validation_reports/t1/7t1z | HTTPS FTP |
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-Related structure data
Related structure data | 7t1yC 2ovpS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 16771.787 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SKP1, EMC19, OCP2, SKP1A, TCEB1L / Production host: Escherichia coli (E. coli) / References: UniProt: P63208 | ||||
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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.) Homo sapiens (human) / Gene: FBXW7, FBW7, FBX30, SEL10 / Production host: Escherichia coli (E. coli) / References: UniProt: Q969H0 | ||||
#3: Protein/peptide | Mass: 2573.770 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) | ||||
#4: Chemical | ChemComp-SO4 / #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 5.54 Å3/Da / Density % sol: 77.8 % |
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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: 123 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å |
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: 2.77→50 Å / Num. obs: 37654 / % possible obs: 100 % / Redundancy: 9.7 % / Biso Wilson estimate: 52.88 Å2 / CC1/2: 0.992 / Net I/σ(I): 12 |
Reflection shell | Resolution: 2.77→2.82 Å / Num. unique obs: 1861 / CC1/2: 0.602 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2ovp Resolution: 2.77→49.96 Å / SU ML: 0.4146 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.1643 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: 55.55 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.77→49.96 Å
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Refine LS restraints |
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LS refinement shell |
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