[English] 日本語
Yorodumi
- EMDB-12369: CryoEM structure of the human Separase-Securin complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-12369
TitleCryoEM structure of the human Separase-Securin complex
Map dataPostprocessed map of human Separase-Securin complex at 2.9A.
Sample
  • Complex: Inhibitory complex of human separase bound to securin.
    • Protein or peptide: Separin
    • Protein or peptide: Securin
Function / homology
Function and homology information


negative regulation of mitotic sister chromatid separation / negative regulation of sister chromatid cohesion / separase / meiotic chromosome 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 mitotic sister chromatid separation / negative regulation of sister chromatid cohesion / separase / meiotic chromosome 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 / chromosome organization / catalytic activity / 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
Securin sister-chromatid separation inhibitor / Securin sister-chromatid separation inhibitor / Peptidase C50, separase / SEPARIN core domain / SEPARIN core domain profile.
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsYu J / Raia P / Ghent CM / Raisch T / Sadian Y / Barford D / Raunser S / Morgan DO / Boland A
Funding support Switzerland, United States, 2 items
OrganizationGrant numberCountry
Swiss National Science Foundation310030_185235 Switzerland
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35-GM118053 United States
CitationJournal: 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
DepositionFeb 14, 2021-
Header (metadata) releaseAug 4, 2021-
Map releaseAug 4, 2021-
UpdateAug 18, 2021-
Current statusAug 18, 2021Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.1
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.1
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-7nj1
  • Surface level: 0.1
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_12369.png

Downloads & links

-
Map

FileDownload / File: emd_12369.map.gz / Format: CCP4 / Size: 122.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPostprocessed map of human Separase-Securin complex at 2.9A.
Voxel sizeX=Y=Z: 1.05 Å
Density
Contour LevelBy AUTHOR: 0.1 / Movie #1: 0.1
Minimum - Maximum-0.028123753 - 1.8777864
Average (Standard dev.)0.0007226745 (±0.017121399)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions318318318
Spacing318318318
CellA=B=C: 333.9 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.051.051.05
M x/y/z318318318
origin x/y/z0.0000.0000.000
length x/y/z333.900333.900333.900
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ450450450
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS318318318
D min/max/mean-0.0281.8780.001

-
Supplemental data

-
Additional map: Unsharpened map of human Separase-Securin complex at 2.9A.

Fileemd_12369_additional_1.map
AnnotationUnsharpened map of human Separase-Securin complex at 2.9A.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: Focus-refined map (postprocessed) of human Separase-Securin complex at...

Fileemd_12369_additional_2.map
AnnotationFocus-refined map (postprocessed) of human Separase-Securin complex at 2.9A.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: Focus-refined map (unsharpened) of human Separase-Securin complex at...

Fileemd_12369_additional_3.map
AnnotationFocus-refined map (unsharpened) of human Separase-Securin complex at 2.9A.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Inhibitory complex of human separase bound to securin.

EntireName: Inhibitory complex of human separase bound to securin.
Components
  • Complex: Inhibitory complex of human separase bound to securin.
    • Protein or peptide: Separin
    • Protein or peptide: Securin

-
Supramolecule #1: Inhibitory complex of human separase bound to securin.

SupramoleculeName: Inhibitory complex of human separase bound to securin.
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)

-
Macromolecule #1: Separin

MacromoleculeName: Separin / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: separase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 237.610469 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: 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

MacromoleculeName: Securin / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 22.05234 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: 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

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.025 mg/mL
BufferpH: 7.8
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GRAPHENE OXIDE / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 293 K / Instrument: LEICA EM GP
DetailsThe sample was monodisperse. We use graphene oxide-coated EM grids.

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Calibrated defocus max: 2.5 µm / Calibrated defocus min: 1.3 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.3 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm 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
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

CTF correctionSoftware: (Name: CTFFIND, Gctf, cryoSPARC)
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionApplied 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

-
Atomic model buiding 1

RefinementProtocol: AB INITIO MODEL
Output model

PDB-7nj1:
CryoEM structure of the human Separase-Securin complex

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more