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- PDB-2ovr: Structure of the Skp1-Fbw7-CyclinEdegN complex -

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Basic information

Entry
Database: PDB / ID: 2ovr
TitleStructure of the Skp1-Fbw7-CyclinEdegN complex
Components
  • F-box/WD repeat protein 7
  • S-phase kinase-associated protein 1A
  • cyclinE N-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 / 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 / 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 / Parkin-FBXW7-Cul1 ubiquitin ligase complex / ubiquitin recycling / ubiquitin-protein transferase activator activity / 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 / Loss of Function of FBXW7 in Cancer and NOTCH1 Signaling / maintenance of protein location in nucleus / positive regulation of proteasomal protein catabolic process / vasculature development / positive regulation of ubiquitin-dependent protein catabolic process / positive regulation of protein targeting to mitochondrion / SCF ubiquitin ligase complex / sister chromatid cohesion / 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 / Association of TriC/CCT with target proteins during biosynthesis / lipid homeostasis / 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 / molecular function activator activity / 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 / 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 / Degradation of beta-catenin by the destruction complex / beta-catenin binding / 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 / Downstream TCR signaling / 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
Monooxygenase - #50 / 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 ...Monooxygenase - #50 / 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 / Monooxygenase / Potassium Channel Kv1.1; Chain A / Potassium Channel Kv1.1; Chain A / 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 / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / 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 / 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: 2.5 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 1.4Apr 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
Revision 1.5Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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 N-terminal degron
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,23615
Polymers68,0843
Non-polymers1,15312
Water3,603200
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6560 Å2
ΔGint-178 kcal/mol
Surface area26930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)232.558, 232.558, 107.659
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11B-6-

HOH

21B-36-

HOH

31B-91-

HOH

41B-159-

HOH

51B-163-

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 N-terminal degron


Mass: 950.990 Da / Num. of mol.: 1 / Fragment: N-terminal / Source method: obtained synthetically / Details: sequence occurs naturally in Homo sapiens
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 200 / Source method: isolated from a natural source / Formula: H2O
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

Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M Hepes-Na, 1.12 M Li2SO4, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 123 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 8-BM / Wavelength: 0.978 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 15, 2004 / Details: mirrors
RadiationMonochromator: YALE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.5→20 Å / Num. all: 51020 / Num. obs: 50357 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.3 % / Biso Wilson estimate: 49.1 Å2 / Rmerge(I) obs: 0.058 / Rsym value: 0.058 / Net I/σ(I): 22.9
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.287 / Mean I/σ(I) obs: 6.9 / Num. unique all: 5011 / Rsym value: 0.287 / % possible all: 99.7

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Processing

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

Resolution: 2.5→19.75 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 451100.61 / 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
Rfree0.251 1966 4 %RANDOM
Rwork0.225 ---
obs0.225 49288 96.8 %-
all-50357 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 34.2716 Å2 / ksol: 0.319045 e/Å3
Displacement parametersBiso mean: 51.3 Å2
Baniso -1Baniso -2Baniso -3
1-3.42 Å20 Å20 Å2
2--3.42 Å20 Å2
3----6.84 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.38 Å0.34 Å
Luzzati d res low-5 Å
Luzzati sigma a0.47 Å0.39 Å
Refinement stepCycle: LAST / Resolution: 2.5→19.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4647 0 60 200 4907
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
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_deg1.8
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.04
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.367 309 3.9 %
Rwork0.333 7579 -
obs--94.2 %
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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