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- PDB-7t1z: Structure of the Fbw7-Skp1-MycNdegron complex -

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Basic information

Entry
Database: PDB / ID: 7t1z
TitleStructure of the Fbw7-Skp1-MycNdegron complex
Components
  • F-box/WD repeat-containing protein 7
  • Myc proto-oncogene N terminal degron
  • S-phase kinase-associated protein 1
KeywordsLIGASE / Ubiquitin ligase / WD40
Function / homology
Function and homology information


negative regulation of SREBP signaling pathway / negative regulation of triglyceride biosynthetic process / negative regulation of hepatocyte proliferation / regulation of lipid storage / ubiquitin recycling / ubiquitin-protein transferase activator activity / Parkin-FBXW7-Cul1 ubiquitin ligase complex / F-box domain binding / regulation of mitophagy / regulation of cell cycle G1/S phase transition ...negative regulation of SREBP signaling pathway / negative regulation of triglyceride biosynthetic process / negative regulation of hepatocyte proliferation / regulation of lipid storage / ubiquitin recycling / ubiquitin-protein transferase activator activity / Parkin-FBXW7-Cul1 ubiquitin ligase complex / F-box domain binding / regulation of mitophagy / 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 / phosphothreonine residue binding / positive regulation of ubiquitin protein ligase activity / Cul7-RING ubiquitin ligase complex / maintenance of protein location in nucleus / positive regulation of proteasomal protein catabolic process / Loss of Function of FBXW7 in Cancer and NOTCH1 Signaling / positive regulation of ubiquitin-dependent protein catabolic process / vasculature development / : / sister chromatid cohesion / SCF ubiquitin ligase complex / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / Prolactin receptor signaling / Association of TriC/CCT with target proteins during biosynthesis / ubiquitin ligase complex scaffold activity / lipid homeostasis / cullin family protein binding / negative regulation of Notch signaling pathway / protein monoubiquitination / positive regulation of epidermal growth factor receptor signaling pathway / ubiquitin-like ligase-substrate adaptor activity / protein K48-linked ubiquitination / : / Nuclear events stimulated by ALK signaling in cancer / molecular function activator activity / cyclin binding / ubiquitin binding / Regulation of BACH1 activity / positive regulation of protein ubiquitination / MAP3K8 (TPL2)-dependent MAPK1/3 activation / 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 / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / Degradation of GLI2 by the proteasome / GLI3 is processed to GLI3R by the proteasome / beta-catenin binding / regulation of circadian rhythm / Degradation of beta-catenin by the destruction complex / NOTCH1 Intracellular Domain Regulates Transcription / CLEC7A (Dectin-1) signaling / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / SCF(Skp2)-mediated degradation of p27/p21 / FCERI mediated NF-kB activation / Interleukin-1 signaling / protein polyubiquitination / Orc1 removal from chromatin / Regulation of RUNX2 expression and activity / Cyclin D associated events in G1 / cellular response to UV / Regulation of PLK1 Activity at G2/M Transition / Downstream TCR signaling / rhythmic process / Antigen processing: Ubiquitination & Proteasome degradation / 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 / DNA damage response / ubiquitin protein ligase binding / centrosome / nucleolus / protein-containing complex / nucleoplasm / identical protein binding / nucleus / cytoplasm / cytosol
Similarity search - Function
A Receptor for Ubiquitination Targets / F-box domain profile. / F-box-like / F-box-like domain superfamily / SKP1 component, dimerisation / S-phase kinase-associated protein 1 / SKP1-like, dimerisation domain superfamily / Skp1 family, dimerisation domain / F-box domain / S-phase kinase-associated protein 1-like ...A Receptor for Ubiquitination Targets / F-box domain profile. / F-box-like / F-box-like domain superfamily / SKP1 component, dimerisation / S-phase kinase-associated protein 1 / SKP1-like, dimerisation domain superfamily / Skp1 family, dimerisation domain / F-box domain / S-phase kinase-associated protein 1-like / SKP1 component, POZ domain / Skp1 family, tetramerisation domain / Found in Skp1 protein family / SKP1/BTB/POZ domain superfamily / WD domain, G-beta repeat / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
S-phase kinase-associated protein 1 / F-box/WD repeat-containing protein 7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.77 Å
AuthorsWang, B. / Rusnac, D.V. / Clurman, B.E. / Zheng, N.
Funding support United States, 1items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: 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
DepositionDec 2, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 16, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: S-phase kinase-associated protein 1
B: F-box/WD repeat-containing protein 7
C: Myc proto-oncogene N terminal degron
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,4118
Polymers70,9303
Non-polymers4805
Water1,78399
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5760 Å2
ΔGint-91 kcal/mol
Surface area26230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)232.869, 232.869, 107.161
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122
Space group name HallI4bw2bw
Symmetry operation#1: x,y,z
#2: -y+1/2,x,z+3/4
#3: y+1/2,-x,z+3/4
#4: x+1/2,-y,-z+3/4
#5: -x+1/2,y,-z+3/4
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z
#9: x+1/2,y+1/2,z+1/2
#10: -y+1,x+1/2,z+5/4
#11: y+1,-x+1/2,z+5/4
#12: x+1,-y+1/2,-z+5/4
#13: -x+1,y+1/2,-z+5/4
#14: -x+1/2,-y+1/2,z+1/2
#15: y+1/2,x+1/2,-z+1/2
#16: -y+1/2,-x+1/2,-z+1/2

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Components

#1: Protein S-phase kinase-associated protein 1 / Cyclin-A/CDK2-associated protein p19 / p19A / Organ of Corti protein 2 / OCP-2 / Organ of Corti ...Cyclin-A/CDK2-associated protein p19 / p19A / Organ of Corti protein 2 / OCP-2 / Organ of Corti protein II / OCP-II / RNA polymerase II elongation factor-like protein / SIII / Transcription elongation factor B polypeptide 1-like / p19skp1


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
#2: Protein F-box/WD repeat-containing protein 7 / Archipelago homolog / hAgo / F-box and WD-40 domain-containing protein 7 / F-box protein FBX30 / ...Archipelago homolog / hAgo / F-box and WD-40 domain-containing protein 7 / F-box protein FBX30 / SEL-10 / hCdc4


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 Myc proto-oncogene N terminal degron


Mass: 2573.770 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 99 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 5.54 Å3/Da / Density % sol: 77.8 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.1 M Bicine pH6.5, 1.6 M Li2SO4

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Data collection

DiffractionMean temperature: 123 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 29, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 2.77→2.82 Å / Num. unique obs: 1861 / CC1/2: 0.602

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ovp

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
RfactorNum. reflection% reflection
Rfree0.2484 1999 5.31 %
Rwork0.2231 35655 -
obs0.2244 37654 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 55.55 Å2
Refinement stepCycle: LAST / Resolution: 2.77→49.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4578 0 25 99 4702
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.02564686
X-RAY DIFFRACTIONf_angle_d1.40376352
X-RAY DIFFRACTIONf_chiral_restr0.0823728
X-RAY DIFFRACTIONf_plane_restr0.0112796
X-RAY DIFFRACTIONf_dihedral_angle_d18.26521709
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.77-2.840.43311400.38162504X-RAY DIFFRACTION99.77
2.84-2.910.33021410.3212512X-RAY DIFFRACTION100
2.91-30.33061420.27742518X-RAY DIFFRACTION100
3-3.10.30731400.25722504X-RAY DIFFRACTION99.96
3.1-3.210.28411420.25282532X-RAY DIFFRACTION100
3.21-3.340.28661410.25562512X-RAY DIFFRACTION100
3.34-3.490.25991410.25382514X-RAY DIFFRACTION99.96
3.49-3.670.25471420.20132539X-RAY DIFFRACTION100
3.67-3.90.21381430.19822539X-RAY DIFFRACTION100
3.9-4.20.22521430.1952538X-RAY DIFFRACTION100
4.2-4.620.20511420.16682558X-RAY DIFFRACTION100
4.63-5.290.20671450.18082570X-RAY DIFFRACTION100
5.3-6.660.26161450.23792605X-RAY DIFFRACTION100
6.67-49.960.21831520.2252710X-RAY DIFFRACTION99.76

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