[English] 日本語
Yorodumi- PDB-7nj0: CryoEM structure of the human Separase-Cdk1-cyclin B1-Cks1 complex -
+Open data
-Basic information
Entry | Database: PDB / ID: 7nj0 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | CryoEM structure of the human Separase-Cdk1-cyclin B1-Cks1 complex | |||||||||
Components |
| |||||||||
Keywords | HYDROLASE / autoinhibition phosphate-binding pocket pseudosubstrate Scc1 | |||||||||
Function / homology | Function and homology information negative regulation of mitotic sister chromatid separation / negative regulation of sister chromatid cohesion / separase / regulation of Schwann cell differentiation / pronuclear fusion / cyclin B1-CDK1 complex / positive regulation of mitochondrial ATP synthesis coupled electron transport / Mitotic Prophase / positive regulation of mitotic sister chromatid segregation / meiotic chromosome separation ...negative regulation of mitotic sister chromatid separation / negative regulation of sister chromatid cohesion / separase / regulation of Schwann cell differentiation / pronuclear fusion / cyclin B1-CDK1 complex / positive regulation of mitochondrial ATP synthesis coupled electron transport / Mitotic Prophase / positive regulation of mitotic sister chromatid segregation / meiotic chromosome separation / histone kinase activity / Golgi disassembly / microtubule cytoskeleton organization involved in mitosis / G2/M DNA replication checkpoint / E2F-enabled inhibition of pre-replication complex formation / ventricular cardiac muscle cell development / Depolymerization of the Nuclear Lamina / positive regulation of attachment of spindle microtubules to kinetochore / MASTL Facilitates Mitotic Progression / regulation of mitotic cell cycle spindle assembly checkpoint / establishment of mitotic spindle localization / Activation of NIMA Kinases NEK9, NEK6, NEK7 / homologous chromosome segregation / Phosphorylation of Emi1 / Phosphorylation of proteins involved in the G2/M transition by Cyclin A:Cdc2 complexes / patched binding / cyclin A2-CDK1 complex / meiotic spindle organization / positive regulation of mitotic metaphase/anaphase transition / Nuclear Pore Complex (NPC) Disassembly / Transcriptional regulation by RUNX2 / outer kinetochore / Phosphorylation of the APC/C / mitotic cell cycle phase transition / Transcription of E2F targets under negative control by p107 (RBL1) and p130 (RBL2) in complex with HDAC1 / Initiation of Nuclear Envelope (NE) Reformation / protein localization to kinetochore / Polo-like kinase mediated events / Golgi Cisternae Pericentriolar Stack Reorganization / cyclin-dependent protein serine/threonine kinase activator activity / chromosome condensation / Condensation of Prometaphase Chromosomes / response to copper ion / centrosome cycle / [RNA-polymerase]-subunit kinase / cyclin-dependent protein serine/threonine kinase regulator activity / SCF ubiquitin ligase complex / mitotic metaphase chromosome alignment / cysteine-type endopeptidase inhibitor activity / G1/S-Specific Transcription / cyclin-dependent protein kinase activity / MAPK3 (ERK1) activation / response to amine / ubiquitin-like protein ligase binding / mitotic sister chromatid segregation / mitotic G2 DNA damage checkpoint signaling / regulation of embryonic development / Regulation of APC/C activators between G1/S and early anaphase / mitotic cytokinesis / cellular response to organic cyclic compound / chromosome organization / cyclin-dependent protein kinase holoenzyme complex / response to axon injury / cyclin-dependent kinase / animal organ regeneration / cyclin-dependent protein serine/threonine kinase activity / response to cadmium ion / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / cysteine-type peptidase activity / catalytic activity / Cyclin A/B1/B2 associated events during G2/M transition / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / positive regulation of cardiac muscle cell proliferation / Recruitment of mitotic centrosome proteins and complexes / ERK1 and ERK2 cascade / Hsp70 protein binding / Resolution of Sister Chromatid Cohesion / Recruitment of NuMA to mitotic centrosomes / epithelial cell differentiation / APC/C:Cdc20 mediated degradation of Cyclin B / Anchoring of the basal body to the plasma membrane / positive regulation of G2/M transition of mitotic cell cycle / regulation of mitotic cell cycle / cyclin binding / positive regulation of mitotic cell cycle / RNA polymerase II CTD heptapeptide repeat kinase activity / AURKA Activation by TPX2 / mitotic spindle organization / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / Condensation of Prophase Chromosomes / positive regulation of DNA replication / response to activity / ubiquitin binding / APC/C:Cdc20 mediated degradation of Securin / molecular function activator activity / spindle microtubule / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / peptidyl-threonine phosphorylation / G1/S transition of mitotic cell cycle Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å | |||||||||
Authors | Yu, J. / Raia, P. / Ghent, C.M. / Raisch, T. / Sadian, Y. / Barford, D. / Raunser, S. / Morgan, D.O. / Boland, A. | |||||||||
Funding support | Switzerland, United States, 2items
| |||||||||
Citation | Journal: Nature / Year: 2021 Title: Structural basis of human separase regulation by securin and CDK1-cyclin B1. Authors: Jun Yu / Pierre Raia / Chloe M Ghent / Tobias Raisch / Yashar Sadian / Simone Cavadini / Pramod M Sabale / David Barford / Stefan Raunser / David O Morgan / Andreas Boland / Abstract: In early mitosis, the duplicated chromosomes are held together by the ring-shaped cohesin complex. Separation of chromosomes during anaphase is triggered by separase-a large cysteine endopeptidase ...In early mitosis, the duplicated chromosomes are held together by the ring-shaped cohesin complex. Separation of chromosomes during anaphase is triggered by separase-a large cysteine endopeptidase that cleaves the cohesin subunit SCC1 (also known as RAD21). Separase is activated by degradation of its inhibitors, securin and cyclin B, but the molecular mechanisms of separase regulation are not clear. Here we used cryogenic electron microscopy to determine the structures of human separase in complex with either securin or CDK1-cyclin B1-CKS1. In both complexes, separase is inhibited by pseudosubstrate motifs that block substrate binding at the catalytic site and at nearby docking sites. As in Caenorhabditis elegans and yeast, human securin contains its own pseudosubstrate motifs. By contrast, CDK1-cyclin B1 inhibits separase by deploying pseudosubstrate motifs from intrinsically disordered loops in separase itself. One autoinhibitory loop is oriented by CDK1-cyclin B1 to block the catalytic sites of both separase and CDK1. Another autoinhibitory loop blocks substrate docking in a cleft adjacent to the separase catalytic site. A third separase loop contains a phosphoserine that promotes complex assembly by binding to a conserved phosphate-binding pocket in cyclin B1. Our study reveals the diverse array of mechanisms by which securin and CDK1-cyclin B1 bind and inhibit separase, providing the molecular basis for the robust control of chromosome segregation. | |||||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7nj0.cif.gz | 352.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7nj0.ent.gz | 272.4 KB | Display | PDB format |
PDBx/mmJSON format | 7nj0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nj/7nj0 ftp://data.pdbj.org/pub/pdb/validation_reports/nj/7nj0 | HTTPS FTP |
---|
-Related structure data
Related structure data | 12368MC 7nj1C M: map data used to model this data C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
|
---|---|
1 |
|
-Components
#1: Protein | Mass: 244677.328 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PTTG1, EAP1, PTTG, TUTR1, ESPL1, ESP1, KIAA0165 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: O95997, UniProt: Q14674, separase |
---|---|
#2: Protein | Mass: 36667.098 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CDK1, CDC2, CDC28A, CDKN1, P34CDC2 / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: P06493, cyclin-dependent kinase, [RNA-polymerase]-subunit kinase |
#3: Protein | Mass: 52625.723 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CCNB1, CCNB / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P14635 |
#4: 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: Spodoptera frugiperda (fall armyworm) / References: UniProt: P61024 |
#5: Chemical | ChemComp-PO4 / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Mutual inhibitory complex of human separase-Cdk1-cyclin B1-Cks1 (CCC) complex. Type: COMPLEX / Entity ID: #1-#4 / Source: RECOMBINANT |
---|---|
Molecular weight | Experimental value: NO |
Source (natural) | Organism: Homo sapiens (human) |
Source (recombinant) | Organism: Spodoptera frugiperda (fall armyworm) |
Buffer solution | pH: 7.8 |
Specimen | Conc.: 0.05 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES Details: The sample was monodisperse. We use graphene oxide-coated EM grids. |
Specimen support | Grid material: GOLD / Grid type: Quantifoil R1.2/1.3 |
Vitrification | Instrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 90 % / Chamber temperature: 293 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
---|---|
Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 105000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 1300 nm / Calibrated defocus min: 1300 nm / Calibrated defocus max: 2500 nm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 3 sec. / Electron dose: 78 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 5 / Num. of real images: 13640 |
-Processing
Software | Name: PHENIX / Version: 1.18rc5_3822: / Classification: refinement | |||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
EM software |
| |||||||||||||||||||||||||||
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | |||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 312836 / Symmetry type: POINT | |||||||||||||||||||||||||||
Atomic model building | Protocol: AB INITIO MODEL | |||||||||||||||||||||||||||
Atomic model building |
| |||||||||||||||||||||||||||
Refine LS restraints |
|