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- PDB-2ovq: Structure of the Skp1-Fbw7-CyclinEdegC complex -

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Basic information

Entry
Database: PDB / ID: 2ovq
TitleStructure of the Skp1-Fbw7-CyclinEdegC complex
Components
  • F-box/WD repeat protein 7
  • S-phase kinase-associated protein 1A
  • cyclinE C-terminal degron
KeywordsTRANSCRIPTION/CELL CYCLE / F-box / WD40 domains / double phosphorylation / TRANSCRIPTION-CELL CYCLE COMPLEX
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 / PcG protein complex / phosphothreonine residue binding / regulation of cell cycle G1/S phase transition / regulation of autophagy of mitochondrion / 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 / protein monoubiquitination / Prolactin receptor signaling / 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 / lung development / Negative regulation of NOTCH4 signaling / Iron uptake and transport / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / 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 / beta-catenin binding / 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 / protein polyubiquitination / Interleukin-1 signaling / 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
Monooxygenase - #50 / 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 ...Monooxygenase - #50 / 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 / Potassium Channel Kv1.1; Chain A / Potassium Channel Kv1.1; Chain A / Monooxygenase / S-phase kinase-associated protein 1-like / SKP1 component, POZ domain / Skp1 family, tetramerisation domain / Found in Skp1 protein family / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / 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 / Up-down Bundle / 2-Layer Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
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: 2.6 Å
AuthorsHao, B. / Oehlmann, S. / Sowa, M.E. / Harper, J.W. / Pavletich, N.P.
CitationJournal: Mol.Cell / Year: 2007
Title: Structure of a Fbw7-Skp1-Cyclin E Complex: Multisite-Phosphorylated Substrate Recognition by SCF Ubiquitin Ligases
Authors: Hao, B. / Oehlmann, S. / Sowa, M.E. / Harper, J.W. / Pavletich, N.P.
History
DepositionFeb 14, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 24, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Oct 18, 2017Group: Refinement description / Category: software
Revision 1.5Apr 3, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: S-phase kinase-associated protein 1A
B: F-box/WD repeat protein 7
C: cyclinE C-terminal degron
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,22711
Polymers68,4593
Non-polymers7698
Water3,207178
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5840 Å2
ΔGint-107 kcal/mol
Surface area27150 Å2
MethodPISA
2
A: S-phase kinase-associated protein 1A
B: F-box/WD repeat protein 7
C: cyclinE C-terminal degron
hetero molecules

A: S-phase kinase-associated protein 1A
B: F-box/WD repeat protein 7
C: cyclinE C-terminal degron
hetero molecules

A: S-phase kinase-associated protein 1A
B: F-box/WD repeat protein 7
C: cyclinE C-terminal degron
hetero molecules

A: S-phase kinase-associated protein 1A
B: F-box/WD repeat protein 7
C: cyclinE C-terminal degron
hetero molecules


Theoretical massNumber of molelcules
Total (without water)276,90944
Polymers273,83512
Non-polymers3,07432
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_556-y,-x,-z+11
crystal symmetry operation10_555-x,-y,z1
crystal symmetry operation15_556y,x,-z+11
Buried area33440 Å2
ΔGint-467 kcal/mol
Surface area98530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)233.066, 233.066, 107.563
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11B-155-

HOH

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Components

#1: Protein S-phase kinase-associated protein 1A / Skp1 / Cyclin A/CDK2-associated protein p19 / p19A / p19skp1 / RNA polymerase II elongation factor- ...Skp1 / Cyclin A/CDK2-associated protein p19 / p19A / p19skp1 / RNA polymerase II elongation factor-like protein / Organ of Corti protein 2 / OCP-II protein / OCP-2 / Transcription elongation factor B / SIII


Mass: 16853.164 Da / Num. of mol.: 1 / Fragment: residues 1-147
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SKP1A, EMC19, OCP2, SKP1, TCEB1L / Plasmid: engineered pGEX vector / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P63208
#2: Protein F-box/WD repeat protein 7 / Fbw7 / F-box and WD-40 domain protein 7 / F-box protein FBX30 / hCdc4 / Archipelago homolog / hAgo / SEL-10


Mass: 50279.410 Da / Num. of mol.: 1 / Fragment: N-terminal residues 263-707
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FBXW7, FBW7, FBX30, SEL10 / Plasmid: engineered pGEX vector / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q969H0
#3: Protein/peptide cyclinE C-terminal degron


Mass: 1326.284 Da / Num. of mol.: 1 / Fragment: C-terminal / Source method: obtained synthetically / Details: sequence occurs naturally in Homo sapiens
#4: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 178 / Source method: isolated from a natural source / Formula: H2O

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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

Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 0.1 M Bicine, 1.4 M Li2SO4, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 123 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9A / Wavelength: 0.9795 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Mar 4, 2004 / Details: mirrors
RadiationMonochromator: YALE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.6→20 Å / Num. all: 45772 / Num. obs: 44674 / % possible obs: 97.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.2 % / Biso Wilson estimate: 49.1 Å2 / Rmerge(I) obs: 0.091 / Rsym value: 0.091 / Net I/σ(I): 14.4
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.363 / Mean I/σ(I) obs: 5.1 / Rsym value: 0.363 / % possible all: 99

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNS1refinement
PDB_EXTRACT2data extraction
ADSCQUANTUMdata collection
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Skp1, b-TrCP1, and Cdc4

Resolution: 2.6→19.76 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 666958.51 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.266 1488 3.5 %RANDOM
Rwork0.232 ---
obs0.232 42657 93.9 %-
all-44674 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 28.8506 Å2 / ksol: 0.310456 e/Å3
Displacement parametersBiso mean: 54.2 Å2
Baniso -1Baniso -2Baniso -3
1-3.43 Å20 Å20 Å2
2--3.43 Å20 Å2
3----6.87 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.42 Å0.36 Å
Luzzati d res low-5 Å
Luzzati sigma a0.45 Å0.4 Å
Refinement stepCycle: LAST / Resolution: 2.6→19.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4678 0 40 178 4896
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.8
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.321.5
X-RAY DIFFRACTIONc_mcangle_it2.242
X-RAY DIFFRACTIONc_scbond_it1.932
X-RAY DIFFRACTIONc_scangle_it2.932.5
LS refinement shellResolution: 2.6→2.76 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.379 225 3.4 %
Rwork0.352 6303 -
obs--87.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.param
X-RAY DIFFRACTION3localtoppa
X-RAY DIFFRACTION4localtoppa
X-RAY DIFFRACTION5ion.param

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