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Yorodumi- EMDB-16327: Cryo-EM structure of SKP1-SKP2-CKS1 from the SCFSKP2 E3 ligase complex -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-16327 | |||||||||
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Title | Cryo-EM structure of SKP1-SKP2-CKS1 from the SCFSKP2 E3 ligase complex | |||||||||
Map data | ||||||||||
Sample |
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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 / autophagic cell death / positive regulation of protein polyubiquitination / negative regulation of epithelial cell proliferation involved in prostate gland development / FOXO-mediated transcription of cell cycle genes / 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 / autophagic cell death / positive regulation of protein polyubiquitination / negative regulation of epithelial cell proliferation involved in prostate gland development / FOXO-mediated transcription of cell cycle genes / 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 / epithelial cell proliferation involved in prostate gland development / mitotic cell cycle phase transition / negative regulation of epithelial cell apoptotic process / negative regulation of cyclin-dependent protein serine/threonine kinase activity / negative regulation of phosphorylation / ubiquitin ligase activator activity / 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 / AKT phosphorylates targets in the cytosol / Cul4A-RING E3 ubiquitin ligase complex / epithelial cell apoptotic process / SCF ubiquitin ligase complex / cellular response to antibiotic / positive regulation of intracellular estrogen receptor signaling pathway / ubiquitin ligase complex scaffold activity / negative regulation of kinase activity / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / cellular response to lithium ion / molecular function inhibitor activity / protein kinase inhibitor activity / p53-Dependent G1 DNA Damage Response / Prolactin receptor signaling / PTK6 Regulates Cell Cycle / regulation of cyclin-dependent protein serine/threonine kinase activity / 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 / Nuclear events stimulated by ALK signaling in cancer / response to amino acid / localization / protein K48-linked ubiquitination / TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest / response to glucose / response to cadmium ion / Cyclin E associated events during G1/S transition / Cyclin A:Cdk2-associated events at S phase entry / positive regulation of microtubule polymerization / regulation of cell migration / Notch signaling pathway / Hsp70 protein binding / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / regulation of mitotic cell cycle / FLT3 Signaling / Regulation of BACH1 activity / cyclin binding / MAP3K8 (TPL2)-dependent MAPK1/3 activation / 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 / placenta development / Degradation of GLI1 by the proteasome / Activation of NF-kappaB in B cells / sensory perception of sound / 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 / 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 / potassium ion transport / negative regulation of cell growth / DNA Damage/Telomere Stress Induced Senescence / G1/S transition of mitotic cell cycle / NOTCH1 Intracellular Domain Regulates Transcription Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.5 Å | |||||||||
Authors | Rowland RJ / Salamina M / Endicott JA / Noble MEM | |||||||||
Funding support | United Kingdom, 1 items
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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
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_16327.map.gz | 97.2 MB | EMDB map data format | |
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Header (meta data) | emd-16327-v30.xml emd-16327.xml | 20.9 KB 20.9 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_16327_fsc.xml | 9.9 KB | Display | FSC data file |
Images | emd_16327.png | 116.9 KB | ||
Masks | emd_16327_msk_1.map | 103 MB | Mask map | |
Others | emd_16327_half_map_1.map.gz emd_16327_half_map_2.map.gz | 95.5 MB 95.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-16327 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-16327 | HTTPS FTP |
-Related structure data
Related structure data | 8bylMC 8byaC 8bzoC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_16327.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.07 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_16327_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_16327_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_16327_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Locally refined complex of SKP1-SKP2-CKS1-p27 from the hexametric...
Entire | Name: Locally refined complex of SKP1-SKP2-CKS1-p27 from the hexametric SCFSKP2 E3 Ligase complex |
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Components |
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-Supramolecule #1: Locally refined complex of SKP1-SKP2-CKS1-p27 from the hexametric...
Supramolecule | Name: Locally refined complex of SKP1-SKP2-CKS1-p27 from the hexametric SCFSKP2 E3 Ligase complex type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 66 KDa |
-Macromolecule #1: S-phase kinase-associated protein 1
Macromolecule | Name: S-phase kinase-associated protein 1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 18.679965 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: MPSIKLQSSD GEIFEVDVEI AKQSVTIKTM LEDLGMDDEG DDDPVPLPNV NAAILKKVIQ WCTHHKDDPP PPEDDENKEK RTDDIPVWD QEFLKVDQGT LFELILAANY LDIKGLLDVT CKTVANMIKG KTPEEIRKTF NIKNDFTEEE EAQVRKENQW C EEK UniProtKB: S-phase kinase-associated protein 1 |
-Macromolecule #2: S-phase kinase-associated protein 2
Macromolecule | Name: S-phase kinase-associated protein 2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 47.817785 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: MHRKHLQEIP DLSSNVATSF TWGWDSSKTS ELLSGMGVSA LEKEEPDSEN IPQELLSNLG HPESPPRKRL KSKGSDKDFV IVRRPKLNR ENFPGVSWDS LPDELLLGIF SCLCLPELLK VSGVCKRWYR LASDESLWQT LDLTGKNLHP DVTGRLLSQG V IAFRCPRS ...String: MHRKHLQEIP DLSSNVATSF TWGWDSSKTS ELLSGMGVSA LEKEEPDSEN IPQELLSNLG HPESPPRKRL KSKGSDKDFV IVRRPKLNR ENFPGVSWDS LPDELLLGIF SCLCLPELLK VSGVCKRWYR LASDESLWQT LDLTGKNLHP DVTGRLLSQG V IAFRCPRS FMDQPLAEHF SPFRVQHMDL SNSVIEVSTL HGILSQCSKL QNLSLEGLRL SDPIVNTLAK NSNLVRLNLS GC SGFSEFA LQTLLSSCSR LDELNLSWCF DFTEKHVQVA VAHVSETITQ LNLSGYRKNL QKSDLSTLVR RCPNLVHLDL SDS VMLKND CFQEFFQLNY LQHLSLSRCY DIIPETLLEL GEIPTLKTLQ VFGIVPDGTL QLLKEALPHL QINCSHFTTI ARPT IGNKK NQEIWGIKCR LTLQKPSCL UniProtKB: S-phase kinase-associated protein 2 |
-Macromolecule #3: Cyclin-dependent kinases regulatory subunit 1
Macromolecule | Name: Cyclin-dependent kinases regulatory subunit 1 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 9.679211 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: MSHKQIYYSD KYDDEEFEYR HVMLPKDIAK LVPKTHLMSE SEWRNLGVQQ SQGWVHYMIH EPEPHILLFR RPLPKKPKK UniProtKB: Cyclin-dependent kinases regulatory subunit 1 |
-Macromolecule #4: Cyclin-dependent kinase inhibitor 1B
Macromolecule | Name: Cyclin-dependent kinase inhibitor 1B / type: protein_or_peptide / ID: 4 / Details: DGSPNAGSVEQ(TPO)PKK / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 22.188303 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: MSNVRVSNGS PSLERMDARQ AEHPKPSACR NLFGPVDHEE LTRDLEKHCR DMEEASQRKW NFDFQNHKPL EGKYEWQEVE KGSLPEFYY RPPRPPKGAC KVPAQESQDV SGSRPAAPLI GAPANSEDTH LVDPKTDPSD SQTGLAEQCA GIRKRPATDD S STQNKRAN ...String: MSNVRVSNGS PSLERMDARQ AEHPKPSACR NLFGPVDHEE LTRDLEKHCR DMEEASQRKW NFDFQNHKPL EGKYEWQEVE KGSLPEFYY RPPRPPKGAC KVPAQESQDV SGSRPAAPLI GAPANSEDTH LVDPKTDPSD SQTGLAEQCA GIRKRPATDD S STQNKRAN RTEENVSDGS PNAGSVEQ(TPO)P KKPGLRRRQT UniProtKB: Cyclin-dependent kinase inhibitor 1B |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.8 |
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Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: OTHER |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 278.15 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 130000 |
Sample stage | Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average exposure time: 9.0 sec. / Average electron dose: 65.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
-Atomic model buiding 1
Details | Initial fitting was performed in chimera followed by real space refinement in Phenix |
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Refinement | Space: REAL / Protocol: RIGID BODY FIT / Overall B value: 122 |
Output model | PDB-8byl: |