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- PDB-2e31: Structural basis for selection of glycosylated substrate by SCFFb... -

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Basic information

Entry
Database: PDB / ID: 2.0E+31
TitleStructural basis for selection of glycosylated substrate by SCFFbs1 ubiquitin ligase
Components
  • F-box only protein 2
  • S-phase kinase-associated protein 1A
KeywordsLIGASE / ubiquitin / SCF / ubiquitin ligase / fbs1
Function / homology
Function and homology information


extrinsic component of postsynaptic membrane / denatured protein binding / regulation of protein catabolic process at postsynapse, modulating synaptic transmission / glycoprotein catabolic process / F-box domain binding / PcG protein complex / Neddylation / Antigen processing: Ubiquitination & Proteasome degradation / positive regulation of ubiquitin protein ligase activity / Cul7-RING ubiquitin ligase complex ...extrinsic component of postsynaptic membrane / denatured protein binding / regulation of protein catabolic process at postsynapse, modulating synaptic transmission / glycoprotein catabolic process / F-box domain binding / PcG protein complex / Neddylation / Antigen processing: Ubiquitination & Proteasome degradation / positive regulation of ubiquitin protein ligase activity / Cul7-RING ubiquitin ligase complex / maintenance of protein location in nucleus / Loss of Function of FBXW7 in Cancer and NOTCH1 Signaling / SCF ubiquitin ligase complex / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / ubiquitin ligase complex scaffold activity / Prolactin receptor signaling / protein monoubiquitination / cullin family protein binding / regulation of protein ubiquitination / ubiquitin-like ligase-substrate adaptor activity / protein K48-linked ubiquitination / Nuclear events stimulated by ALK signaling in cancer / ERAD pathway / Regulation of BACH1 activity / MAP3K8 (TPL2)-dependent MAPK1/3 activation / molecular function activator activity / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / Vpu mediated degradation of CD4 / Dectin-1 mediated noncanonical NF-kB signaling / Iron uptake and transport / Activation of NF-kappaB in B cells / Degradation of GLI1 by the proteasome / Negative regulation of NOTCH4 signaling / 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 / Degradation of beta-catenin by the destruction complex / 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 / Orc1 removal from chromatin / protein polyubiquitination / Regulation of RUNX2 expression and activity / Cyclin D associated events in G1 / Regulation of PLK1 Activity at G2/M Transition / Circadian Clock / Antigen processing: Ubiquitination & Proteasome degradation / Downstream TCR signaling / Neddylation / amyloid-beta binding / ubiquitin-dependent protein catabolic process / carbohydrate binding / proteasome-mediated ubiquitin-dependent protein catabolic process / dendritic spine / protein ubiquitination / chromatin remodeling / protein domain specific binding / negative regulation of cell population proliferation / centrosome / glutamatergic synapse / endoplasmic reticulum / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
F-box associated (FBA) domain / F-box only protein / F-box associated region / F-box-associated (FBA) domain profile. / F-box associated region / F-box domain / Monooxygenase - #50 / F-box domain profile. / SKP1 component, dimerisation / S-phase kinase-associated protein 1 ...F-box associated (FBA) domain / F-box only protein / F-box associated region / F-box-associated (FBA) domain profile. / F-box associated region / F-box domain / Monooxygenase - #50 / F-box domain profile. / SKP1 component, dimerisation / S-phase kinase-associated protein 1 / F-box-like domain superfamily / SKP1-like, dimerisation domain superfamily / Skp1 family, dimerisation domain / F-box-like / 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 / Galactose-binding domain-like / SKP1/BTB/POZ domain superfamily / Galactose-binding-like domain superfamily / Jelly Rolls / Up-down Bundle / Sandwich / 2-Layer Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
S-phase kinase-associated protein 1 / F-box only protein 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIR-AS, MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsMizushima, T. / Yoshida, Y. / Kumanomidou, T. / Hasegawa, Y. / Yamane, T. / Tanaka, K.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2007
Title: Structural basis for the selection of glycosylated substrates by SCFFbs1 ubiquitin ligase
Authors: Mizushima, T. / Yoshida, Y. / Kumanomidou, T. / Hasegawa, Y. / Suzuki, A. / Yamane, T. / Tanaka, K.
History
DepositionNov 20, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 20, 2007Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Remark 300 BIOMOLECULE THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). ... BIOMOLECULE THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). This molecule is a part of the SCF complex, which is a hetero tetramer generated by Skp1-Fbs1-Cul1-Rbx1.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: F-box only protein 2
B: S-phase kinase-associated protein 1A


Theoretical massNumber of molelcules
Total (without water)52,6492
Polymers52,6492
Non-polymers00
Water39622
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3200 Å2
ΔGint-26 kcal/mol
Surface area18750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.408, 106.408, 109.854
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein F-box only protein 2 / Fbs1


Mass: 33676.762 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: PET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(RIL) / References: UniProt: Q80UW2
#2: Protein S-phase kinase-associated protein 1A / Cyclin A/CDK2-associated protein p19 / p19A / p19skp1 / RNA polymerase II elongation factor-like ...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 / Skp1


Mass: 18972.279 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(RIL) / References: UniProt: P63208
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 22 / 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

CrystalDensity Matthews: 3.41 Å3/Da / Density % sol: 63.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.7
Details: 2.0M ammonium sulphate, 0.1M sodium citrate, 30mM chitobiose, pH 5.7, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: Bruker DIP-6040 / Detector: CCD / Date: Oct 9, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.4→109.8 Å / Num. obs: 27964 / % possible obs: 97.7 % / Observed criterion σ(I): 0 / Redundancy: 5.4 % / Biso Wilson estimate: 52.83 Å2 / Rmerge(I) obs: 0.045 / Net I/σ(I): 18.1
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.327 / Mean I/σ(I) obs: 2.7 / % possible all: 93

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
RefinementMethod to determine structure: SIR-AS, MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1LDK and 1UMH

1ldk

1umh


Resolution: 2.4→53.22 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.899 / SU B: 8.204 / SU ML: 0.191 / Cross valid method: THROUGHOUT / ESU R: 0.267 / ESU R Free: 0.244 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29136 1425 5.1 %RANDOM
Rwork0.23334 ---
obs0.23605 26521 97.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 66.935 Å2
Baniso -1Baniso -2Baniso -3
1-0.11 Å20.06 Å20 Å2
2--0.11 Å20 Å2
3----0.17 Å2
Refinement stepCycle: LAST / Resolution: 2.4→53.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3055 0 0 22 3077
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0223126
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3511.9524244
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3825374
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.36625.159157
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.26515535
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1421516
X-RAY DIFFRACTIONr_chiral_restr0.0980.2462
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022389
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.220.21431
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3050.22110
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1370.2109
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1520.228
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1410.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6561.51919
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.22623042
X-RAY DIFFRACTIONr_scbond_it1.40631388
X-RAY DIFFRACTIONr_scangle_it2.4254.51202
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.356 97 -
Rwork0.315 1846 -
obs--92.48 %

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