+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-12369 | |||||||||
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Title | CryoEM structure of the human Separase-Securin complex | |||||||||
Map data | Postprocessed map of human Separase-Securin complex at 2.9A. | |||||||||
Sample |
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Function / homology | Function and homology information negative regulation of sister chromatid cohesion / separase / meiotic chromosome separation / mitotic sister chromatid separation / establishment of mitotic spindle localization / homologous chromosome segregation / meiotic spindle organization / positive regulation of mitotic metaphase/anaphase transition / cysteine-type endopeptidase inhibitor activity / mitotic sister chromatid segregation ...negative regulation of sister chromatid cohesion / separase / meiotic chromosome separation / mitotic sister chromatid separation / establishment of mitotic spindle localization / homologous chromosome segregation / meiotic spindle organization / positive regulation of mitotic metaphase/anaphase transition / cysteine-type endopeptidase inhibitor activity / mitotic sister chromatid segregation / mitotic cytokinesis / catalytic activity / chromosome organization / cysteine-type peptidase activity / APC/C:Cdc20 mediated degradation of Securin / molecular function activator activity / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / mitotic spindle / SH3 domain binding / Separation of Sister Chromatids / spermatogenesis / cell division / cysteine-type endopeptidase activity / DNA repair / centrosome / apoptotic process / proteolysis / nucleus / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.9 Å | |||||||||
Authors | Yu J / Raia P / Ghent CM / Raisch T / Sadian Y / Barford D / Raunser S / Morgan DO / Boland A | |||||||||
Funding support | Switzerland, United States, 2 items
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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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_12369.map.gz | 104.7 MB | EMDB map data format | |
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Header (meta data) | emd-12369-v30.xml emd-12369.xml | 22.4 KB 22.4 KB | Display Display | EMDB header |
Images | emd_12369.png | 91 KB | ||
Others | emd_12369_additional_1.map.gz emd_12369_additional_2.map.gz emd_12369_additional_3.map.gz | 96.1 MB 104.6 MB 96.1 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-12369 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-12369 | HTTPS FTP |
-Validation report
Summary document | emd_12369_validation.pdf.gz | 195.6 KB | Display | EMDB validaton report |
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Full document | emd_12369_full_validation.pdf.gz | 194.7 KB | Display | |
Data in XML | emd_12369_validation.xml.gz | 6.5 KB | Display | |
Data in CIF | emd_12369_validation.cif.gz | 7.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-12369 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-12369 | HTTPS FTP |
-Related structure data
Related structure data | 7nj1MC 7nj0C M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_12369.map.gz / Format: CCP4 / Size: 122.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Postprocessed map of human Separase-Securin complex at 2.9A. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.05 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: Unsharpened map of human Separase-Securin complex at 2.9A.
File | emd_12369_additional_1.map | ||||||||||||
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Annotation | Unsharpened map of human Separase-Securin complex at 2.9A. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Focus-refined map (postprocessed) of human Separase-Securin complex at...
File | emd_12369_additional_2.map | ||||||||||||
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Annotation | Focus-refined map (postprocessed) of human Separase-Securin complex at 2.9A. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Focus-refined map (unsharpened) of human Separase-Securin complex at...
File | emd_12369_additional_3.map | ||||||||||||
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Annotation | Focus-refined map (unsharpened) of human Separase-Securin complex at 2.9A. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Inhibitory complex of human separase bound to securin.
Entire | Name: Inhibitory complex of human separase bound to securin. |
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Components |
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-Supramolecule #1: Inhibitory complex of human separase bound to securin.
Supramolecule | Name: Inhibitory complex of human separase bound to securin. type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
-Macromolecule #1: Separin
Macromolecule | Name: Separin / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: separase |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 237.610469 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: MRSFKRVNFG TLLSSQKEAE ELLPDLKEFL SNPPAGFPSS RSDAERRQAC DAILRACNQQ LTAKLACPRH LGSLLELAEL ACDGYLVST PQRPPLYLER ILFVLLRNAA AQGSPEVTLR LAQPLHACLV QCSREAAPQD YEAVARGSFS LLWKGAEALL E RRAAFAAR ...String: MRSFKRVNFG TLLSSQKEAE ELLPDLKEFL SNPPAGFPSS RSDAERRQAC DAILRACNQQ LTAKLACPRH LGSLLELAEL ACDGYLVST PQRPPLYLER ILFVLLRNAA AQGSPEVTLR LAQPLHACLV QCSREAAPQD YEAVARGSFS LLWKGAEALL E RRAAFAAR LKALSFLVLL EDESTPCEVP HFASPTACRA VAAHQLFDAS GHGLNEADAD FLDDLLSRHV IRALVGERGS SS GLLSPQR ALCLLELTLE HCRRFCWSRH HDKAISAVEK AHSYLRNTNL APSLQLCQLG VKLLQVGEEG PQAVAKLLIK ASA VLSKSM EAPSPPLRAL YESCQFFLSG LERGTKRRYR LDAILSLFAF LGGYCSLLQQ LRDDGVYGGS SKQQQSFLQM YFQG LHLYT VVVYDFAQGC QIVDLADLTQ LVDSCKSTVV WMLEALEGLS GQELTDHMGM TASYTSNLAY SFYSHKLYAE ACAIS EPLC QHLGLVKPGT YPEVPPEKLH RCFRLQVESL KKLGKQAQGC KMVILWLAAL QPCSPEHMAE PVTFWVRVKM DAARAG DKE LQLKTLRDSL SGWDPETLAL LLREELQAYK AVRADTGQER FNIICDLLEL SPEETPAGAW ARATHLVELA QVLCYHD FT QQTNCSALDA IREALQLLDS VRPEAQARDQ LLDDKAQALL WLYICTLEAK IQEGIERDRR AQAPGNLEEF EVNDLNYE D KLQEDRFLYS NIAFNLAADA AQSKCLDQAL ALWKELLTKG QAPAVRCLQQ TAASLQILAA LYQLVAKPMQ ALEVLLLLR IVSERLKDHS KAAGSSCHIT QLLLTLGCPS YAQLHLEEAA SSLKHLDQTT DTYLLLSLTC DLLRSQLYWT HQKVTKGVSL LLSVLRDPA LQKSSKAWYL LRVQVLQLVA AYLSLPSNNL SHSLWEQLCA QGWQTPEIAL IDSHKLLRSI ILLLMGSDIL S TQKAAVET SFLDYGENLV QKWQVLSEVL SCSEKLVCHL GRLGSVSEAK AFCLEALKLT TKLQIPRQCA LFLVLKGELE LA RNDIDLC QSDLQQVLFL LESCTEFGGV TQHLDSVKKV HLQKGKQQAQ VPCPPQLPEE ELFLRGPALE LVATVAKEPG PIA PSTNSS PVLKTKPQPI PNFLSHSPTC DCSLCASPVL TAVCLRWVLV TAGVRLAMGH QAQGLDLLQV VLKGCPEAAE RLTQ ALQAS LNHKTPPSLV PSLLDEILAQ AYTLLALEGL NQPSNESLQK VLQSGLKFVA ARIPHLEPWR ASLLLIWALT KLGGL SCCT TQLFASSWGW QPPLIKSVPG SEPSKTQGQK RSGRGRQKLA SAPLSLNNTS QKGLEGRGLP CTPKPPDRIR QAGPHV PFT VFEEVCPTES KPEVPQAPRV QQRVQTRLKV NFSDDSDLED PVSAEAWLAE EPKRRGTASR GRGRARKGLS LKTDAVV AP GSAPGNPGLN GRSRRAKKVA SRHCEERRPQ RASDQARPGP EIMRTIPEEE LTDNWRKMSF EILRGSDGED SASGGKTP A PGPEAASGEW ELLRLDSSKK KLPSPCPDKE SDKDLGPRLQ LPSAPVATGL STLDSICDSL SVAFRGISHC PPSGLYAHL CRFLALCLGH RDPYATAFLV TESVSITCRH QLLTHLHRQL SKAQKHRGSL EIADQLQGLS LQEMPGDVPL ARIQRLFSFR ALESGHFPQ PEKESFQERL ALIPSGVTVC VLALATLQPG TVGNTLLLTR LEKDSPPVSV QIPTGQNKLH LRSVLNEFDA I QKAQKENS SCTDKREWWT GRLALDHRME VLIASLEKSV LGCWKGLLLP SSEEPGPAQE ASRLQELLQD CGWKYPDRTL LK IMLSGAG ALTPQDIQAL AYGLCPTQPE RAQELLNEAV GRLQGLTVPS NSHLVLVLDK DLQKLPWESM PSLQALPVTR LPS FRFLLS YSIIKEYGAS PVLSQGVDPR STFYVLNPHN NLSSTEEQFR ANFSSEAGWR GVVGEVPRPE QVQEALTKHD LYIY AGHGA GARFLDGQAV LRLSCRAVAL LFGCSSAALA VHGNLEGAGI VLKYIMAGCP LFLGNLWDVT DRDIDRYTEA LLQGW LGAG PGAPLLYYVN QARQAPRLKY LIGAAPIAYG LPVSLRSSLA EENLYFQSWS HPQFEKGGGS GGGSGGGSWS HPQFEK |
-Macromolecule #2: Securin
Macromolecule | Name: Securin / 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: 22.05234 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: MATLIYVDKE NGEPGTRVVA KDGLKLGSGP SIKALDGRSQ VSTPRFGKTF DAPPALPKAT RKALGTVNRA TEKSVKTKGP LKQKQPSFS AKKMTEKTVK AKSSVPASDD AYPEIEKFFP FNPLDFESFD LPEEHQIAHL PLSGVPLMIL DEERELEKLF Q LGPPSPVK ...String: MATLIYVDKE NGEPGTRVVA KDGLKLGSGP SIKALDGRSQ VSTPRFGKTF DAPPALPKAT RKALGTVNRA TEKSVKTKGP LKQKQPSFS AKKMTEKTVK AKSSVPASDD AYPEIEKFFP FNPLDFESFD LPEEHQIAHL PLSGVPLMIL DEERELEKLF Q LGPPSPVK MPSPPWESNL LQSPSSILST LDVELPPVCC DIDI |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.025 mg/mL |
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Buffer | pH: 7.8 |
Grid | Model: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GRAPHENE OXIDE / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 293 K / Instrument: LEICA EM GP |
Details | The sample was monodisperse. We use graphene oxide-coated EM grids. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 4 / Number real images: 16540 / Average exposure time: 3.0 sec. / Average electron dose: 67.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Calibrated defocus max: 2.5 µm / Calibrated defocus min: 1.3 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.3 µm / Nominal magnification: 105000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
CTF correction | Software: (Name: CTFFIND, Gctf, cryoSPARC) |
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Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 205300 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |
-Atomic model buiding 1
Refinement | Protocol: AB INITIO MODEL |
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Output model | PDB-7nj1: |