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- PDB-2ast: Crystal structure of Skp1-Skp2-Cks1 in complex with a p27 peptide -
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Open data
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Basic information
Entry | Database: PDB / ID: 2ast | ||||||
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Title | Crystal structure of Skp1-Skp2-Cks1 in complex with a p27 peptide | ||||||
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![]() | LIGASE/LIGASE INHIBITOR / SCF-substrate complex / LRR / CELL CYCLE / PROTEIN TURNOVER COMPLEX / LIGASE-LIGASE INHIBITOR complex | ||||||
Function / homology | ![]() cyclin-dependent protein kinase activating kinase regulator activity / regulation of lens fiber cell differentiation / negative regulation of cardiac muscle tissue regeneration / negative regulation of cyclin-dependent protein kinase activity / positive regulation of protein polyubiquitination / autophagic cell death / FOXO-mediated transcription of cell cycle genes / negative regulation of epithelial cell proliferation involved in prostate gland development / F-box domain binding / Aberrant regulation of mitotic exit in cancer due to RB1 defects ...cyclin-dependent protein kinase activating kinase regulator activity / regulation of lens fiber cell differentiation / negative regulation of cardiac muscle tissue regeneration / negative regulation of cyclin-dependent protein kinase activity / positive regulation of protein polyubiquitination / autophagic cell death / FOXO-mediated transcription of cell cycle genes / negative regulation of epithelial cell proliferation involved in prostate gland development / F-box domain binding / Aberrant regulation of mitotic exit in cancer due to RB1 defects / PcG protein complex / regulation of cell cycle G1/S phase transition / regulation of exit from mitosis / mitotic cell cycle phase transition / epithelial cell proliferation involved in prostate gland development / negative regulation of epithelial cell apoptotic process / negative regulation of cyclin-dependent protein serine/threonine kinase activity / ubiquitin ligase activator activity / negative regulation of phosphorylation / Cul7-RING ubiquitin ligase complex / positive regulation of ubiquitin protein ligase activity / cyclin-dependent protein serine/threonine kinase inhibitor activity / Loss of Function of FBXW7 in Cancer and NOTCH1 Signaling / maintenance of protein location in nucleus / RHO GTPases activate CIT / cyclin-dependent protein serine/threonine kinase activator activity / nuclear export / positive regulation of intracellular estrogen receptor signaling pathway / AKT phosphorylates targets in the cytosol / Cul4A-RING E3 ubiquitin ligase complex / epithelial cell apoptotic process / SCF ubiquitin ligase complex / cellular response to antibiotic / ubiquitin ligase complex scaffold activity / negative regulation of kinase activity / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / regulation of cyclin-dependent protein serine/threonine kinase activity / molecular function inhibitor activity / cellular response to lithium ion / protein kinase inhibitor activity / p53-Dependent G1 DNA Damage Response / Prolactin receptor signaling / PTK6 Regulates Cell Cycle / Constitutive Signaling by AKT1 E17K in Cancer / regulation of G1/S transition of mitotic cell cycle / protein monoubiquitination / negative regulation of vascular associated smooth muscle cell proliferation / Defective binding of RB1 mutants to E2F1,(E2F2, E2F3) / cullin family protein binding / protein K63-linked ubiquitination / inner ear development / cellular response to organic cyclic compound / ubiquitin-like ligase-substrate adaptor activity / positive regulation of double-strand break repair via homologous recombination / negative regulation of mitotic cell cycle / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / cyclin-dependent protein kinase holoenzyme complex / localization / response to amino acid / protein K48-linked ubiquitination / Nuclear events stimulated by ALK signaling in cancer / TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest / response to glucose / Cyclin E associated events during G1/S transition / response to cadmium ion / Cyclin A:Cdk2-associated events at S phase entry / Notch signaling pathway / regulation of cell migration / positive regulation of microtubule polymerization / regulation of mitotic cell cycle / Hsp70 protein binding / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / FLT3 Signaling / Regulation of BACH1 activity / MAP3K8 (TPL2)-dependent MAPK1/3 activation / cyclin binding / positive regulation of DNA replication / ubiquitin binding / 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 / sensory perception of sound / 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 / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / potassium ion transport / Degradation of beta-catenin by the destruction complex / placenta development / DNA Damage/Telomere Stress Induced Senescence / NOTCH1 Intracellular Domain Regulates Transcription / negative regulation of cell growth / CLEC7A (Dectin-1) signaling Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Hao, B. / Zhang, N. / Schulman, B.A. / Wu, G. / Pagano, M. / Pavletich, N.P. | ||||||
![]() | ![]() Title: Structural Basis of the Cks1-Dependent Recognition of p27(Kip1) by the SCF(Skp2) Ubiquitin Ligase. Authors: Hao, B. / Zheng, N. / Schulman, B.A. / Wu, G. / Miller, J.J. / Pagano, M. / Pavletich, N.P. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 132.5 KB | Display | ![]() |
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PDB format | ![]() | 100.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 474.9 KB | Display | ![]() |
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Full document | ![]() | 483.8 KB | Display | |
Data in XML | ![]() | 24.7 KB | Display | |
Data in CIF | ![]() | 35 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2assC ![]() 1fqvS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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3 | ![]()
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Unit cell |
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Components
-S-phase kinase-associated protein ... , 2 types, 2 molecules AB
#1: Protein | Mass: 18135.324 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Protein | Mass: 37923.691 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
-Cyclin-dependent ... , 2 types, 2 molecules CD
#3: Protein | Mass: 8482.662 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#4: Protein/peptide | Mass: 1126.154 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: Chemical synthesis, this sequence occurs naturally in humans. ![]() |
-Non-polymers , 2 types, 267 molecules ![](data/chem/img/BEN.gif)
![](data/chem/img/HOH.gif)
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#5: Chemical | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.9 Å3/Da / Density % sol: 75 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: PEG8K, 5% benzamidine, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 173 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RIGAKU / Detector: IMAGE PLATE / Date: Aug 8, 2005 / Details: mirrors |
Radiation | Monochromator: YALE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97946 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→20 Å / Num. all: 55849 / Num. obs: 55849 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.5 % / Rmerge(I) obs: 0.056 / Rsym value: 0.056 / Net I/σ(I): 35 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 6 % / Rmerge(I) obs: 0.422 / Mean I/σ(I) obs: 4 / Num. unique all: 5513 / Rsym value: 0.422 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 1FQV Resolution: 2.3→20 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.945 / SU B: 4.448 / SU ML: 0.109 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.174 / ESU R Free: 0.154 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 57.844 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.303→2.362 Å / Total num. of bins used: 20
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