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- PDB-1fs1: INSIGHTS INTO SCF UBIQUITIN LIGASES FROM THE STRUCTURE OF THE SKP... -

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Basic information

Entry
Database: PDB / ID: 1fs1
TitleINSIGHTS INTO SCF UBIQUITIN LIGASES FROM THE STRUCTURE OF THE SKP1-SKP2 COMPLEX
Components
  • CYCLIN A/CDK2-ASSOCIATED P19
  • CYCLIN A/CDK2-ASSOCIATED P45
KeywordsLIGASE / Skp1 / Skp2 / F-box / LRR / leucine-rich repeat / SCF / ubiquitin / E3 / ubiquitin protein ligase
Function / homology
Function and homology information


positive regulation of protein polyubiquitination / F-box domain binding / cellular response to cell-matrix adhesion / Aberrant regulation of mitotic exit in cancer due to RB1 defects / PcG protein complex / 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 / SCF ubiquitin ligase complex ...positive regulation of protein polyubiquitination / F-box domain binding / cellular response to cell-matrix adhesion / Aberrant regulation of mitotic exit in cancer due to RB1 defects / PcG protein complex / 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 / SCF ubiquitin ligase complex / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / positive regulation of intracellular estrogen receptor signaling pathway / ubiquitin ligase complex scaffold activity / Prolactin receptor signaling / cullin family protein binding / protein K63-linked ubiquitination / protein monoubiquitination / ubiquitin-like ligase-substrate adaptor activity / protein K48-linked ubiquitination / positive regulation of double-strand break repair via homologous recombination / Nuclear events stimulated by ALK signaling in cancer / positive regulation of smooth muscle cell proliferation / Regulation of BACH1 activity / molecular function activator activity / MAP3K8 (TPL2)-dependent MAPK1/3 activation / 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 / G1/S transition of mitotic cell cycle / 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 / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / 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 / G2/M transition of mitotic cell cycle / 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 / Downstream TCR signaling / Antigen processing: Ubiquitination & Proteasome degradation / Neddylation / regulation of apoptotic process / defense response to virus / proteasome-mediated ubiquitin-dependent protein catabolic process / regulation of cell cycle / Ub-specific processing proteases / protein ubiquitination / chromatin remodeling / protein domain specific binding / innate immune response / centrosome / nucleolus / nucleoplasm / identical protein binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Monooxygenase - #50 / A Receptor for Ubiquitination Targets / Leucine-rich repeat, cysteine-containing subtype / Leucine-rich repeat - CC (cysteine-containing) subfamily / 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 ...Monooxygenase - #50 / A Receptor for Ubiquitination Targets / Leucine-rich repeat, cysteine-containing subtype / Leucine-rich repeat - CC (cysteine-containing) subfamily / 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 / Leucine-rich repeat domain superfamily / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
S-phase kinase-associated protein 1 / S-phase kinase-associated protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.8 Å
AuthorsSchulman, B.A. / Carrano, A.C. / Jeffrey, P.D. / Bowen, Z. / Kinnucan, E.R.E. / Finnin, M.S. / Elledge, S.J. / Harper, J.W. / Pagano, M. / Pavletich, N.P.
CitationJournal: Nature / Year: 2000
Title: Insights into SCF ubiquitin ligases from the structure of the Skp1-Skp2 complex.
Authors: Schulman, B.A. / Carrano, A.C. / Jeffrey, P.D. / Bowen, Z. / Kinnucan, E.R. / Finnin, M.S. / Elledge, S.J. / Harper, J.W. / Pagano, M. / Pavletich, N.P.
History
DepositionSep 8, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 29, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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: CYCLIN A/CDK2-ASSOCIATED P19
B: CYCLIN A/CDK2-ASSOCIATED P45
C: CYCLIN A/CDK2-ASSOCIATED P19
D: CYCLIN A/CDK2-ASSOCIATED P45


Theoretical massNumber of molelcules
Total (without water)44,2374
Polymers44,2374
Non-polymers00
Water10,269570
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.540, 41.600, 87.230
Angle α, β, γ (deg.)90.00, 93.42, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein CYCLIN A/CDK2-ASSOCIATED P19 / SKP2 F-BOX


Mass: 6105.007 Da / Num. of mol.: 2 / Fragment: RESIDUES 101-153
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: Q13309
#2: Protein CYCLIN A/CDK2-ASSOCIATED P45 / SKP1


Mass: 16013.290 Da / Num. of mol.: 2 / Fragment: RESIDUES 1-147
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P63208
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 570 / 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: 1.9 Å3/Da / Density % sol: 35.41 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: PEG 1500, sodium acetate, ammonium acetate, DTT, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 25 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
136-38 %PEG15001reservoir
20.1 Msodium acetate1reservoir
30.2 Mammonium acetate1reservoir
45 mMdithiothreitol1reservoir

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9A / Wavelength: 1.072
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.072 Å / Relative weight: 1
Reflection
*PLUS
Highest resolution: 1.8 Å / Num. obs: 29068 / % possible obs: 84.4 % / Num. measured all: 206639 / Rmerge(I) obs: 0.037
Reflection shell
*PLUS
% possible obs: 47.1 % / Rmerge(I) obs: 0.124 / Mean I/σ(I) obs: 6.7

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Processing

Software
NameClassification
MLPHAREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 1.8→8 Å / Rfactor Rfree: 0.274 / Rfactor Rwork: 0.218 / σ(F): 0
Refinement stepCycle: LAST / Resolution: 1.8→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2497 0 0 719 3216
Software
*PLUS
Name: CNS / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.015
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg1.89
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shell
*PLUS
Rfactor Rfree: 0.343 / Rfactor Rwork: 0.286

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