[English] 日本語
Yorodumi- PDB-2ast: Crystal structure of Skp1-Skp2-Cks1 in complex with a p27 peptide -
+Open data
-Basic information
Entry | Database: PDB / ID: 2ast | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of Skp1-Skp2-Cks1 in complex with a p27 peptide | ||||||
Components |
| ||||||
Keywords | LIGASE/LIGASE INHIBITOR / SCF-substrate complex / LRR / CELL CYCLE / PROTEIN TURNOVER COMPLEX / LIGASE-LIGASE INHIBITOR complex | ||||||
Function / homology | Function and homology information 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 / PTK6 Regulates Cell Cycle / autophagic cell death / FOXO-mediated transcription of cell cycle genes / F-box domain binding / negative regulation of epithelial cell proliferation involved in prostate gland development ...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 / PTK6 Regulates Cell Cycle / autophagic cell death / FOXO-mediated transcription of cell cycle genes / F-box domain binding / negative regulation of epithelial cell proliferation involved in prostate gland development / Defective binding of RB1 mutants to E2F1,(E2F2, E2F3) / PcG protein complex / Aberrant regulation of mitotic exit in cancer due to RB1 defects / p53-Dependent G1 DNA Damage Response / 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 / negative regulation of phosphorylation / Cul7-RING ubiquitin ligase complex / positive regulation of ubiquitin protein ligase activity / ubiquitin ligase activator activity / Loss of Function of FBXW7 in Cancer and NOTCH1 Signaling / maintenance of protein location in nucleus / cyclin-dependent protein serine/threonine kinase inhibitor activity / negative regulation of vascular associated smooth muscle cell proliferation / RHO GTPases activate CIT / cyclin-dependent protein serine/threonine kinase activator activity / nuclear export / negative regulation of mitotic cell cycle / AKT phosphorylates targets in the cytosol / positive regulation of intracellular estrogen receptor signaling pathway / Cul4A-RING E3 ubiquitin ligase complex / epithelial cell apoptotic process / SCF ubiquitin ligase complex / cellular response to antibiotic / Cyclin E associated events during G1/S transition / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / ubiquitin ligase complex scaffold activity / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / negative regulation of kinase activity / regulation of cyclin-dependent protein serine/threonine kinase activity / molecular function inhibitor activity / TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest / cellular response to lithium ion / positive regulation of DNA replication / protein kinase inhibitor activity / Prolactin receptor signaling / Cyclin A:Cdk2-associated events at S phase entry / cyclin-dependent protein kinase holoenzyme complex / protein monoubiquitination / Constitutive Signaling by AKT1 E17K in Cancer / regulation of mitotic cell cycle / regulation of G1/S transition of mitotic cell cycle / cullin family protein binding / inner ear development / protein K63-linked ubiquitination / cellular response to organic cyclic compound / cyclin binding / positive regulation of double-strand break repair via homologous recombination / ubiquitin-like ligase-substrate adaptor activity / response to amino acid / protein K48-linked ubiquitination / Nuclear events stimulated by ALK signaling in cancer / response to glucose / response to cadmium ion / Notch signaling pathway / positive regulation of microtubule polymerization / Hsp70 protein binding / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / FLT3 Signaling / regulation of cell migration / Regulation of BACH1 activity / MAP3K8 (TPL2)-dependent MAPK1/3 activation / potassium ion transport / DNA Damage/Telomere Stress Induced Senescence / ubiquitin binding / molecular function activator activity / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / placenta development / Vpu mediated degradation of CD4 / Dectin-1 mediated noncanonical NF-kB signaling / SCF(Skp2)-mediated degradation of p27/p21 / sensory perception of sound / 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 / Orc1 removal from chromatin / 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 / Cyclin D associated events in G1 / G1/S transition of mitotic cell cycle Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Hao, B. / Zhang, N. / Schulman, B.A. / Wu, G. / Pagano, M. / Pavletich, N.P. | ||||||
Citation | Journal: Mol.Cell / Year: 2005 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2ast.cif.gz | 132.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2ast.ent.gz | 100.4 KB | Display | PDB format |
PDBx/mmJSON format | 2ast.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2ast_validation.pdf.gz | 474.9 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 2ast_full_validation.pdf.gz | 483.8 KB | Display | |
Data in XML | 2ast_validation.xml.gz | 24.7 KB | Display | |
Data in CIF | 2ast_validation.cif.gz | 35 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/as/2ast ftp://data.pdbj.org/pub/pdb/validation_reports/as/2ast | HTTPS FTP |
-Related structure data
Related structure data | 2assC 1fqvS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
3 |
| ||||||||
Unit cell |
|
-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.) Homo sapiens (human) / Gene: SKP1A, EMC19, OCP2, SKP1, TCEB1L / Plasmid: pGEX4T1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / Keywords: Skp1 / References: UniProt: P63208 |
---|---|
#2: Protein | Mass: 37923.691 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SKP2, FBXL1 / Plasmid: pGEX4T1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / Keywords: Skp2 / References: UniProt: Q13309 |
-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.) Homo sapiens (human) / Gene: CKS1, CKS1B / Plasmid: pGEX4T3 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / Keywords: Cks1 / References: UniProt: P61024 |
---|---|
#4: Protein/peptide | Mass: 1126.154 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: Chemical synthesis, this sequence occurs naturally in humans. Keywords: p27 peptide / References: UniProt: P46527 |
-Non-polymers , 2 types, 267 molecules
#5: Chemical | #6: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 4.9 Å3/Da / Density % sol: 75 % |
---|---|
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 |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97946 Å |
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 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→20 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.303→2.362 Å / Total num. of bins used: 20
|