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- PDB-3wso: Crystal structure of the Skp1-FBG3 complex -

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Basic information

Entry
Database: PDB / ID: 3wso
TitleCrystal structure of the Skp1-FBG3 complex
Components
  • F-box only protein 44
  • S-phase kinase-associated protein 1
KeywordsLIGASE / F-box protein / SCF ubiquitin ligase / Skp1
Function / homology
Function and homology information


glycoprotein catabolic process / F-box domain binding / PcG protein complex / Cul7-RING ubiquitin ligase complex / positive regulation of ubiquitin protein ligase activity / maintenance of protein location in nucleus / Loss of Function of FBXW7 in Cancer and NOTCH1 Signaling / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / SCF ubiquitin ligase complex / ubiquitin ligase complex scaffold activity ...glycoprotein catabolic process / F-box domain binding / PcG protein complex / Cul7-RING ubiquitin ligase complex / positive regulation of ubiquitin protein ligase activity / maintenance of protein location in nucleus / Loss of Function of FBXW7 in Cancer and NOTCH1 Signaling / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / SCF ubiquitin ligase complex / ubiquitin ligase complex scaffold activity / Prolactin receptor signaling / protein monoubiquitination / cullin family protein binding / ubiquitin-like ligase-substrate adaptor activity / protein K48-linked ubiquitination / Nuclear events stimulated by ALK signaling in cancer / : / Regulation of BACH1 activity / post-translational protein modification / MAP3K8 (TPL2)-dependent MAPK1/3 activation / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / molecular function activator activity / Vpu mediated degradation of CD4 / proteasomal protein catabolic process / 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 / 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 / protein polyubiquitination / Orc1 removal from chromatin / Regulation of RUNX2 expression and activity / Cyclin D associated events in G1 / Regulation of PLK1 Activity at G2/M Transition / Antigen processing: Ubiquitination & Proteasome degradation / Circadian Clock / Downstream TCR signaling / Neddylation / proteasome-mediated ubiquitin-dependent protein catabolic process / protein ubiquitination / chromatin remodeling / protein domain specific binding / centrosome / 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 / Monooxygenase - #50 / A Receptor for Ubiquitination Targets / F-box domain profile. / F-box-like domain superfamily / F-box-like ...F-box associated (FBA) domain / F-box only protein / F-box associated region / F-box-associated (FBA) domain profile. / F-box associated region / 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 / 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 44
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsKumanomidou, T. / Nishio, K. / Takagi, K. / Nakagawa, T. / Suzuki, A. / Yamane, T. / Tokunaga, F. / Iwai, K. / Murakami, A. / Yoshida, Y. ...Kumanomidou, T. / Nishio, K. / Takagi, K. / Nakagawa, T. / Suzuki, A. / Yamane, T. / Tokunaga, F. / Iwai, K. / Murakami, A. / Yoshida, Y. / Tanaka, K. / Mizushima, T.
CitationJournal: Plos One / Year: 2015
Title: The Structural Differences between a Glycoprotein Specific F-Box Protein Fbs1 and Its Homologous Protein FBG3
Authors: Kumanomidou, T. / Nishio, K. / Takagi, K. / Nakagawa, T. / Suzuki, A. / Yamane, T. / Tokunaga, F. / Iwai, K. / Murakami, A. / Yoshida, Y. / Tanaka, K. / Mizushima, T.
History
DepositionMar 18, 2014Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 25, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 28, 2015Group: Database references
Revision 1.2Nov 11, 2015Group: Other
Revision 1.3Nov 8, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: F-box only protein 44
B: S-phase kinase-associated protein 1


Theoretical massNumber of molelcules
Total (without water)48,8532
Polymers48,8532
Non-polymers00
Water28816
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3210 Å2
ΔGint-26 kcal/mol
Surface area20030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.120, 76.594, 193.939
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein F-box only protein 44 / F-box protein FBX30 / F-box/G-domain protein 3


Mass: 29880.842 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FBXO44, FBG3, FBX30, FBX44, FBX6A, FBXO6A / Production host: Escherichia coli (E. coli) / References: UniProt: Q9H4M3
#2: Protein S-phase kinase-associated protein 1 / / Cyclin-A/CDK2-associated protein p19 / Organ of Corti protein 2 / OCP-2 / Organ of Corti protein II ...Cyclin-A/CDK2-associated protein p19 / 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 / p19A / p19skp1


Mass: 18972.279 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
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsACCORDING TO UNIPROT SEQUENCE DATABASE, THERE IS A G->R SEQUENCE CONFLICT AT THIS POSITION.

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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: 2.59 Å3/Da / Density % sol: 52.58 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 8% 2-propanol, 16% PEG4000, 0.1M Na PIPES , pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 288K

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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: Jul 8, 2006
RadiationMonochromator: double-crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.6→97.1 Å / Num. obs: 16474 / % possible obs: 99.5 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 19.8
Reflection shellResolution: 2.6→2.65 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.308 / % possible all: 99.6

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Processing

Software
NameVersionClassification
MOLREPphasing
REFMAC5.8.0049refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Starting model: 2.0E+31 / Resolution: 2.6→60.08 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.907 / SU B: 11.137 / SU ML: 0.24 / Cross valid method: THROUGHOUT / ESU R: 0.601 / ESU R Free: 0.321 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2656 826 5.1 %RANDOM
Rwork0.20464 ---
obs0.20767 15516 99.15 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 56.529 Å2
Baniso -1Baniso -2Baniso -3
1-2.98 Å2-0 Å2-0 Å2
2---2.42 Å2-0 Å2
3----0.56 Å2
Refinement stepCycle: LAST / Resolution: 2.6→60.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3205 0 0 16 3221
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0193290
X-RAY DIFFRACTIONr_bond_other_d0.0010.023072
X-RAY DIFFRACTIONr_angle_refined_deg1.631.9434473
X-RAY DIFFRACTIONr_angle_other_deg0.8737090
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4695387
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.80424.788165
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.0415564
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.881517
X-RAY DIFFRACTIONr_chiral_restr0.0970.2483
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213681
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02758
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2324.6341568
X-RAY DIFFRACTIONr_mcbond_other1.2334.6321567
X-RAY DIFFRACTIONr_mcangle_it2.1376.9341953
X-RAY DIFFRACTIONr_mcangle_other2.1366.9371954
X-RAY DIFFRACTIONr_scbond_it2.734.7081737
X-RAY DIFFRACTIONr_scbond_other2.7294.711738
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.897.0022541
X-RAY DIFFRACTIONr_long_range_B_refined5.20336.5123856
X-RAY DIFFRACTIONr_long_range_B_other5.20236.5233857
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.444 52 -
Rwork0.282 1076 -
obs--95.35 %

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