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- PDB-1fqv: Insights into scf ubiquitin ligases from the structure of the skp... -

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Basic information

Entry
Database: PDB / ID: 1fqv
TitleInsights into scf ubiquitin ligases from the structure of the skp1-skp2 complex
Components
  • SKP1S-phase kinase-associated protein 1
  • SKP2
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 / Aberrant regulation of mitotic exit in cancer due to RB1 defects / 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 ...positive regulation of protein polyubiquitination / F-box domain binding / Aberrant regulation of mitotic exit in cancer due to RB1 defects / 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 / positive regulation of intracellular estrogen receptor signaling pathway / 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 / 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 / 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 / G1/S transition of mitotic cell cycle / 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 / 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 / G2/M transition of mitotic cell cycle / 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 / defense response to virus / regulation of apoptotic process / protein ubiquitination / regulation of cell cycle / Ub-specific processing proteases / chromatin remodeling / protein domain specific binding / innate immune response / centrosome / nucleolus / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Leucine-rich repeat, cysteine-containing subtype / Leucine-rich repeat - CC (cysteine-containing) subfamily / 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 ...Leucine-rich repeat, cysteine-containing subtype / Leucine-rich repeat - CC (cysteine-containing) subfamily / 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 / S-phase kinase-associated protein 1-like / SKP1 component, POZ domain / Skp1 family, tetramerisation domain / Found in Skp1 protein family / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / Alpha-Beta Horseshoe / SKP1/BTB/POZ domain superfamily / Leucine-rich repeat domain superfamily / 2-Layer Sandwich / 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: 2.8 Å
AuthorsSchulman, 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.
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 6, 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: SKP2
B: SKP1
C: SKP2
D: SKP1
E: SKP2
F: SKP1
G: SKP2
H: SKP1
I: SKP2
J: SKP1
K: SKP2
L: SKP1
M: SKP2
N: SKP1
O: SKP2
P: SKP1


Theoretical massNumber of molelcules
Total (without water)438,21516
Polymers438,21516
Non-polymers00
Water0
1
A: SKP2
B: SKP1


Theoretical massNumber of molelcules
Total (without water)54,7772
Polymers54,7772
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2980 Å2
ΔGint-29 kcal/mol
Surface area20410 Å2
MethodPISA
2
C: SKP2
D: SKP1


Theoretical massNumber of molelcules
Total (without water)54,7772
Polymers54,7772
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2910 Å2
ΔGint-29 kcal/mol
Surface area20500 Å2
MethodPISA
3
E: SKP2
F: SKP1


Theoretical massNumber of molelcules
Total (without water)54,7772
Polymers54,7772
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2890 Å2
ΔGint-28 kcal/mol
Surface area20540 Å2
MethodPISA
4
G: SKP2
H: SKP1


Theoretical massNumber of molelcules
Total (without water)54,7772
Polymers54,7772
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2920 Å2
ΔGint-29 kcal/mol
Surface area20470 Å2
MethodPISA
5
I: SKP2
J: SKP1


Theoretical massNumber of molelcules
Total (without water)54,7772
Polymers54,7772
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2930 Å2
ΔGint-29 kcal/mol
Surface area20430 Å2
MethodPISA
6
K: SKP2
L: SKP1


Theoretical massNumber of molelcules
Total (without water)54,7772
Polymers54,7772
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2870 Å2
ΔGint-28 kcal/mol
Surface area20530 Å2
MethodPISA
7
M: SKP2
N: SKP1


Theoretical massNumber of molelcules
Total (without water)54,7772
Polymers54,7772
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2940 Å2
ΔGint-28 kcal/mol
Surface area20500 Å2
MethodPISA
8
O: SKP2
P: SKP1


Theoretical massNumber of molelcules
Total (without water)54,7772
Polymers54,7772
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2930 Å2
ΔGint-30 kcal/mol
Surface area20410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)262.700, 148.200, 133.300
Angle α, β, γ (deg.)90.00, 120.03, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
SKP2 / / CYCLIN A/CDK2-ASSOCIATED PROTEIN P45


Mass: 37923.691 Da / Num. of mol.: 8 / Fragment: 101-436
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
SKP1 / S-phase kinase-associated protein 1 / CYCLIN A/CDK2-ASSOCIATED PROTEIN P19


Mass: 16853.164 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / 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: 2.56 Å3/Da / Density % sol: 52.01 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG 4000, Tris-Cl, ammonium acetate, DTT, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / Details: microseeding and macroseeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
115-16 %PEG40001reservoir
20.1 MTris-HCl1reservoir
30.2 Mammonium acetate1reservoir
410 mMdithiothreitol1reservoir

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.909
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.909 Å / Relative weight: 1
ReflectionResolution: 2.8→8 Å / Num. obs: 90445
Reflection
*PLUS
Highest resolution: 2.8 Å / Num. obs: 108372 / % possible obs: 93.7 % / Num. measured all: 598299 / Rmerge(I) obs: 0.074
Reflection shell
*PLUS
% possible obs: 93.8 % / Rmerge(I) obs: 0.194 / Mean I/σ(I) obs: 5.1

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
RefinementResolution: 2.8→8 Å / σ(F): 2
RfactorNum. reflection
Rfree0.314 3618
Rwork0.275 -
all-103914
obs-90445
Refinement stepCycle: LAST / Resolution: 2.8→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms29256 0 0 0 29256
Software
*PLUS
Name: CNS / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg1.56
LS refinement shell
*PLUS
Rfactor Rfree: 0.429 / Rfactor Rwork: 0.353

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