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- PDB-2e32: Structural basis for selection of glycosylated substrate by SCFFb... -

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Basic information

Entry
Database: PDB / ID: 2.0E+32
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 / glycoprotein catabolic process / F-box domain binding / PcG protein complex / Neddylation / regulation of protein catabolic process at postsynapse, modulating synaptic transmission / positive regulation of ubiquitin protein ligase activity / Cul7-RING ubiquitin ligase complex / maintenance of protein location in nucleus ...extrinsic component of postsynaptic membrane / denatured protein binding / glycoprotein catabolic process / F-box domain binding / PcG protein complex / Neddylation / regulation of protein catabolic process at postsynapse, modulating synaptic transmission / 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 / Antigen processing: Ubiquitination & Proteasome degradation / SCF ubiquitin ligase complex / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / ubiquitin ligase complex scaffold activity / Prolactin receptor signaling / cullin family protein binding / protein monoubiquitination / 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 / 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 / Iron uptake and transport / 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 / beta-catenin binding / NOTCH1 Intracellular Domain Regulates Transcription / CLEC7A (Dectin-1) signaling / SCF(Skp2)-mediated degradation of p27/p21 / FCERI mediated NF-kB activation / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / 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 / : / Antigen processing: Ubiquitination & Proteasome degradation / Downstream TCR signaling / amyloid-beta binding / Neddylation / carbohydrate binding / ubiquitin-dependent protein catabolic process / 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. / 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 / F-box domain / Monooxygenase - #50 / 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 / 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 / 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 / MOLECULAR REPLACEMENT / Resolution: 3.52 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_ncs_dom_lim / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ref_seq_dif.details
Remark 300 BIOMOLECULE THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 4 CHAIN(S). ... BIOMOLECULE THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 4 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). Each 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
C: F-box only protein 2
D: S-phase kinase-associated protein 1A


Theoretical massNumber of molelcules
Total (without water)105,2984
Polymers105,2984
Non-polymers00
Water00
1
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
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2750 Å2
ΔGint-22 kcal/mol
Surface area18270 Å2
MethodPISA
2
C: F-box only protein 2
D: S-phase kinase-associated protein 1A


Theoretical massNumber of molelcules
Total (without water)52,6492
Polymers52,6492
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2790 Å2
ΔGint-23 kcal/mol
Surface area18220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.942, 109.816, 153.040
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
31A
41C
12B
22D
32B
42D
52B
62D

NCS domain segments:

Refine code: 1

Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111GLUGLUPROPROAA49 - 10349 - 103
211GLUGLUPROPROCC49 - 10349 - 103
321HISHISPROPROAA113 - 297113 - 297
421HISHISPROPROCC113 - 297113 - 297
112PROPROASPASPBB2 - 335 - 36
212PROPROASPASPDD2 - 335 - 36
322ASPASPASPASPBB43 - 6846 - 71
422ASPASPASPASPDD43 - 6846 - 71
532ASPASPARGARGBB83 - 15486 - 157
632ASPASPARGARGDD83 - 15486 - 157

NCS ensembles :
ID
1
2

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Components

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


Mass: 33676.762 Da / Num. of mol.: 2
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.: 2
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

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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: 2.63 Å3/Da / Density % sol: 53.23 %
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: Jan 29, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 3.5→152.5 Å / Num. obs: 12279 / % possible obs: 85.2 % / Observed criterion σ(I): 0 / Redundancy: 2.6 % / Biso Wilson estimate: 26.74 Å2 / Rmerge(I) obs: 0.103 / Net I/σ(I): 7
Reflection shellResolution: 3.5→3.63 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.225 / Mean I/σ(I) obs: 4.1 / % possible all: 79

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2E31

2e31


Resolution: 3.52→56.53 Å / Cor.coef. Fo:Fc: 0.892 / Cor.coef. Fo:Fc free: 0.809 / SU B: 36.134 / SU ML: 0.579 / Cross valid method: THROUGHOUT / ESU R Free: 0.772 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29855 651 5 %RANDOM
Rwork0.22259 ---
obs0.22651 12269 89.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 51.038 Å2
Baniso -1Baniso -2Baniso -3
1--4.24 Å20 Å20 Å2
2--3.69 Å20 Å2
3---0.56 Å2
Refinement stepCycle: LAST / Resolution: 3.52→56.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5970 0 0 0 5970
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0226110
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0781.958298
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.5095730
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.46525.163306
X-RAY DIFFRACTIONr_dihedral_angle_3_deg24.536151040
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7981530
X-RAY DIFFRACTIONr_chiral_restr0.1270.2904
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024664
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.3070.23578
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3460.24185
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2020.2330
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.380.293
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3920.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7151.53741
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.32125942
X-RAY DIFFRACTIONr_scbond_it1.75432730
X-RAY DIFFRACTIONr_scangle_it2.9924.52356
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1948tight positional0.090.05
2B1037tight positional0.080.05
1A1948tight thermal0.410.5
2B1037tight thermal0.120.5
LS refinement shellResolution: 3.516→3.608 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.338 56 -
Rwork0.248 823 -
obs--84.6 %

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