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- PDB-3l2o: Structure-Based Mechanism of Dimerization-Dependent Ubiquitinatio... -

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Basic information

Entry
Database: PDB / ID: 3l2o
TitleStructure-Based Mechanism of Dimerization-Dependent Ubiquitination by the SCFFbx4 Ubiquitin Ligase
Components
  • F-box only protein 4
  • S-phase kinase-associated protein 1
KeywordsPROTEIN BINDING/CELL CYCLE / small G protein fold / Ubl conjugation pathway / ubiquitin protein ligase / PROTEIN BINDING-CELL CYCLE complex
Function / homology
Function and homology information


positive regulation of protein polyubiquitination / common myeloid progenitor cell proliferation / F-box domain binding / PcG protein complex / cellular homeostasis / maintenance of protein location in nucleus / Cul7-RING ubiquitin ligase complex / regulation of DNA damage checkpoint / Loss of Function of FBXW7 in Cancer and NOTCH1 Signaling / ubiquitin ligase activator activity ...positive regulation of protein polyubiquitination / common myeloid progenitor cell proliferation / F-box domain binding / PcG protein complex / cellular homeostasis / maintenance of protein location in nucleus / Cul7-RING ubiquitin ligase complex / regulation of DNA damage checkpoint / Loss of Function of FBXW7 in Cancer and NOTCH1 Signaling / ubiquitin ligase activator activity / negative regulation of protein localization to nucleus / post-transcriptional regulation of gene expression / SCF ubiquitin ligase complex / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / Prolactin receptor signaling / Association of TriC/CCT with target proteins during biosynthesis / ubiquitin ligase complex scaffold activity / cullin family protein binding / protein monoubiquitination / ubiquitin ligase complex / negative regulation of fibroblast proliferation / ubiquitin-like ligase-substrate adaptor activity / Nuclear events stimulated by ALK signaling in cancer / positive regulation of telomere maintenance via telomerase / protein K48-linked ubiquitination / telomere maintenance / molecular function activator activity / positive regulation of protein ubiquitination / Regulation of BACH1 activity / MAP3K8 (TPL2)-dependent MAPK1/3 activation / cellular response to ionizing radiation / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / regulation of protein stability / Vpu mediated degradation of CD4 / Dectin-1 mediated noncanonical NF-kB signaling / Degradation of CRY and PER proteins / Activation of NF-kappaB in B cells / Iron uptake and transport / Degradation of GLI1 by the proteasome / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / Negative regulation of NOTCH4 signaling / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / Ubiquitin-Mediated Degradation of Phosphorylated Cdc25A / Degradation of GLI2 by the proteasome / GLI3 is processed to GLI3R by the proteasome / beta-catenin binding / NOTCH1 Intracellular Domain Regulates Transcription / Degradation of beta-catenin by the destruction complex / protein destabilization / CLEC7A (Dectin-1) signaling / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / SCF(Skp2)-mediated degradation of p27/p21 / FCERI mediated NF-kB activation / Interleukin-1 signaling / Orc1 removal from chromatin / protein polyubiquitination / Cyclin D associated events in G1 / cellular senescence / ubiquitin-protein transferase activity / Regulation of RUNX2 expression and activity / ubiquitin protein ligase activity / Regulation of PLK1 Activity at G2/M Transition / Downstream TCR signaling / Antigen processing: Ubiquitination & Proteasome degradation / Neddylation / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / protein ubiquitination / chromatin remodeling / protein domain specific binding / centrosome / protein homodimerization activity / nucleoplasm / nucleus / cytoplasm / cytosol
Similarity search - Function
F-box only protein 4 / Monooxygenase - #50 / F-box domain / 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 ...F-box only protein 4 / Monooxygenase - #50 / F-box domain / 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 / P-loop containing nucleotide triphosphate hydrolases / Up-down Bundle / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
S-phase kinase-associated protein 1 / F-box only protein 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.8 Å
AuthorsLi, Y. / Hao, B.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Structural basis of dimerization-dependent ubiquitination by the SCF(Fbx4) ubiquitin ligase.
Authors: Li, Y. / Hao, B.
History
DepositionDec 15, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 23, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 13, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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 1
B: F-box only protein 4


Theoretical massNumber of molelcules
Total (without water)52,6762
Polymers52,6762
Non-polymers00
Water1,36976
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2920 Å2
ΔGint-23 kcal/mol
Surface area23240 Å2
MethodPISA
2
A: S-phase kinase-associated protein 1
B: F-box only protein 4

A: S-phase kinase-associated protein 1
B: F-box only protein 4


Theoretical massNumber of molelcules
Total (without water)105,3524
Polymers105,3524
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_645y+1,x-1,-z1
Buried area8730 Å2
ΔGint-70 kcal/mol
Surface area43590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.194, 92.194, 148.068
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

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


Mass: 16827.127 Da / Num. of mol.: 1
Mutation: deletion: 38-43, 70-81; P2A; insertion: GGSG between 69 and 82
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EMC19, OCP2, SKP1, SKP1A, TCEB1L / Plasmid: pGEX / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P63208
#2: Protein F-box only protein 4


Mass: 35848.684 Da / Num. of mol.: 1 / Fragment: Fbx4 residues 55-387 / Mutation: deletion: 150-170
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FBX4, FBXO4 / Plasmid: pGEX / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9UKT5
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 76 / 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: 3.45 Å3/Da / Density % sol: 64.33 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 1.5-2 M sodium chloride, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
1,21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSLS X3A11.0721
SYNCHROTRONNSLS X29A21.0809
Detector
TypeIDDetectorDateDetails (eV)
MAR CCD 165 mm1CCDApr 17, 2008mirrors
ADSC QUANTUM 3152CCDOct 3, 2008mirrors
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1YALE MIRRORSSINGLE WAVELENGTHMx-ray1
2YALE MIRRORSSINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.07211
21.08091
ReflectionResolution: 2.8→50 Å / Num. all: 17477 / Num. obs: 17477 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14.3 % / Biso Wilson estimate: 84.1 Å2 / Rmerge(I) obs: 0.086 / Rsym value: 0.086 / Net I/σ(I): 31.5
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 14.3 % / Rmerge(I) obs: 0.856 / Mean I/σ(I) obs: 2.2 / Num. unique all: 1843 / Rsym value: 0.856 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
SHELXSphasing
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.8→50 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.912 / SU B: 38.305 / SU ML: 0.333 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.678 / ESU R Free: 0.372
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29488 915 5 %RANDOM
Rwork0.24945 ---
obs0.25171 17477 99.52 %-
all-17477 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.752 Å2
Baniso -1Baniso -2Baniso -3
1-3.89 Å21.95 Å20 Å2
2--3.89 Å20 Å2
3----5.84 Å2
Refinement stepCycle: LAST / Resolution: 2.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3349 0 0 76 3425
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0223425
X-RAY DIFFRACTIONr_bond_other_d0.0020.022283
X-RAY DIFFRACTIONr_angle_refined_deg1.9271.9584651
X-RAY DIFFRACTIONr_angle_other_deg1.02635598
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.0475412
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.125.125160
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.72715589
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8731514
X-RAY DIFFRACTIONr_chiral_restr0.0650.2526
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0213743
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02653
X-RAY DIFFRACTIONr_mcbond_it0.561.52090
X-RAY DIFFRACTIONr_mcbond_other0.0891.5835
X-RAY DIFFRACTIONr_mcangle_it1.07323392
X-RAY DIFFRACTIONr_scbond_it1.46131335
X-RAY DIFFRACTIONr_scangle_it2.4194.51259
LS refinement shellResolution: 2.8→2.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.466 82 -
Rwork0.388 1240 -
obs-1240 100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
17.5617-5.3184-0.77267.2631.64736.5632-0.862-1.8277-1.15391.13970.64431.11211.3584-0.42940.21780.51820.20840.04650.84510.12720.4067102.149429.175463.7807
27.4704-3.4441-2.011612.27161.92987.73160.1462-0.1445-0.0651-0.25260.11330.61050.2825-0.2117-0.25950.12840.152-0.10120.3165-0.06630.1307108.231838.030750.0442
36.7175-0.9561-5.05194.84372.452611.3841-0.28870.0887-0.5859-0.43750.3458-1.05570.27771.4387-0.05710.28610.1519-0.07260.7099-0.18170.5478120.629929.084638.7606
42.85131.2654.58241.56161.583510.45380.24810.4254-0.2980.20250.2755-0.38211.20260.9713-0.52360.32960.2616-0.06070.415-0.1230.3318112.37724.239833.1861
59.4302-1.35971.683813.4489-1.509113.22620.29210.0335-0.87440.12250.0036-0.17531.46170.2469-0.29560.48910.1695-0.06690.5733-0.10740.4996105.534418.612423.692
68.37350.5963-0.42442.60131.791712.05980.0046-1.03210.11360.68310.07520.11590.2977-0.3244-0.07970.4890.1055-0.08340.17410.01150.2665125.495910.50760.6525
74.0039-0.35061.66944.11820.73647.7440.0541-0.48310.03510.63680.02950.32230.4398-0.8983-0.08360.2607-0.03320.02680.12920.00240.1783115.920710.1495-8.7059
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1002 - 1064
2X-RAY DIFFRACTION2A1065 - 1106
3X-RAY DIFFRACTION3A1107 - 1160
4X-RAY DIFFRACTION4B54 - 119
5X-RAY DIFFRACTION5B120 - 174
6X-RAY DIFFRACTION6B175 - 275
7X-RAY DIFFRACTION7B276 - 383

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