[English] 日本語
Yorodumi
- PDB-7t1z: Structure of the Fbw7-Skp1-MycNdegron complex -

+
Open data


ID or keywords:

Loading...

-
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 / regulation of cell migration involved in sprouting angiogenesis / negative regulation of hepatocyte proliferation / positive regulation of epidermal growth factor-activated receptor activity / regulation of lipid storage / Parkin-FBXW7-Cul1 ubiquitin ligase complex / ubiquitin-protein transferase activator activity / F-box domain binding / ubiquitin recycling ...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 / positive regulation of epidermal growth factor-activated receptor activity / regulation of lipid storage / Parkin-FBXW7-Cul1 ubiquitin ligase complex / ubiquitin-protein transferase activator activity / F-box domain binding / ubiquitin recycling / 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 / positive regulation of ubiquitin-protein transferase activity / sister chromatid cohesion / 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 / rhythmic process / Cyclin D associated events in G1 / 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 / chromosome / Neddylation / 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
A Receptor for Ubiquitination Targets / F-box domain profile. / F-box-like domain superfamily / F-box-like / 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 domain superfamily / F-box-like / 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 / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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 / Sulfate


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


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

-
Experimental details

-
Experiment

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

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more