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Yorodumi- PDB-8byl: Cryo-EM structure of SKP1-SKP2-CKS1 from the SCFSKP2 E3 ligase complex -
+Open data
-Basic information
Entry | Database: PDB / ID: 8byl | ||||||
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Title | Cryo-EM structure of SKP1-SKP2-CKS1 from the SCFSKP2 E3 ligase complex | ||||||
Components |
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Keywords | CELL CYCLE / cyclin-dependent kinase / signalling / ubiquitinationCell cycle | ||||||
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 | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å | ||||||
Authors | Rowland, R.J. / Salamina, M. / Endicott, J.A. / Noble, M.E.M. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Sci Rep / Year: 2023 Title: Cryo-EM structure of SKP1-SKP2-CKS1 in complex with CDK2-cyclin A-p27KIP1. Authors: Rhianna J Rowland / Richard Heath / Daniel Maskell / Rebecca F Thompson / Neil A Ranson / James N Blaza / Jane A Endicott / Martin E M Noble / Marco Salamina / Abstract: p27KIP1 (cyclin-dependent kinase inhibitor 1B, p27) is a member of the CIP/KIP family of CDK (cyclin dependent kinase) regulators that inhibit cell cycle CDKs. p27 phosphorylation by CDK1/2, signals ...p27KIP1 (cyclin-dependent kinase inhibitor 1B, p27) is a member of the CIP/KIP family of CDK (cyclin dependent kinase) regulators that inhibit cell cycle CDKs. p27 phosphorylation by CDK1/2, signals its recruitment to the SCF (S-phase kinase associated protein 1 (SKP1)-cullin-SKP2) E3 ubiquitin ligase complex for proteasomal degradation. The nature of p27 binding to SKP2 and CKS1 was revealed by the SKP1-SKP2-CKS1-p27 phosphopeptide crystal structure. Subsequently, a model for the hexameric CDK2-cyclin A-CKS1-p27-SKP1-SKP2 complex was proposed by overlaying an independently determined CDK2-cyclin A-p27 structure. Here we describe the experimentally determined structure of the isolated CDK2-cyclin A-CKS1-p27-SKP1-SKP2 complex at 3.4 Å global resolution using cryogenic electron microscopy. This structure supports previous analysis in which p27 was found to be structurally dynamic, transitioning from disordered to nascent secondary structure on target binding. We employed 3D variability analysis to further explore the conformational space of the hexameric complex and uncovered a previously unidentified hinge motion centred on CKS1. This flexibility gives rise to open and closed conformations of the hexameric complex that we propose may contribute to p27 regulation by facilitating recognition with SCF. This 3D variability analysis further informed particle subtraction and local refinement approaches to enhance the local resolution of the complex. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8byl.cif.gz | 124.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8byl.ent.gz | 93.8 KB | Display | PDB format |
PDBx/mmJSON format | 8byl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8byl_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 8byl_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 8byl_validation.xml.gz | 34.5 KB | Display | |
Data in CIF | 8byl_validation.cif.gz | 48.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/by/8byl ftp://data.pdbj.org/pub/pdb/validation_reports/by/8byl | HTTPS FTP |
-Related structure data
Related structure data | 16327MC 8byaC 8bzoC C: citing same article (ref.) M: map data used to model this data |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 18679.965 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SKP1, EMC19, OCP2, SKP1A, TCEB1L / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLYSs / References: UniProt: P63208 |
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#2: Protein | Mass: 47817.785 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SKP2, FBXL1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLYSs / References: UniProt: Q13309 |
#3: Protein | Mass: 9679.211 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CKS1B, CKS1, PNAS-143, PNAS-16 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLYSs / References: UniProt: P61024 |
#4: Protein | Mass: 22188.303 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: DGSPNAGSVEQ(TPO)PKK / Source: (gene. exp.) Homo sapiens (human) / Gene: CDKN1B, KIP1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLYSs / References: UniProt: P46527 |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Locally refined complex of SKP1-SKP2-CKS1-p27 from the hexametric SCFSKP2 E3 Ligase complex Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Molecular weight | Value: 0.066 MDa / Experimental value: NO |
Source (natural) | Organism: Homo sapiens (human) |
Source (recombinant) | Organism: Escherichia coli (E. coli) |
Buffer solution | pH: 7.8 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R1.2/1.3 |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 278.15 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 130000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm |
Specimen holder | Cryogen: NITROGEN |
Image recording | Average exposure time: 9 sec. / Electron dose: 65 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 1110356 | ||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 136325 / Num. of class averages: 1 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||
Atomic model building | B value: 122 / Protocol: RIGID BODY FIT / Space: REAL Details: Initial fitting was performed in chimera followed by real space refinement in Phenix | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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