[English] 日本語
Yorodumi
- EMDB-12368: CryoEM structure of the human Separase-Cdk1-cyclin B1-Cks1 complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-12368
TitleCryoEM structure of the human Separase-Cdk1-cyclin B1-Cks1 complex
Map dataSeparase-Cdk1-cyclin B1-Cks1 complex (postprocessed).
Sample
  • Complex: Mutual inhibitory complex of human separase-Cdk1-cyclin B1-Cks1 (CCC) complex.
    • Protein or peptide: Securin,Separin
    • Protein or peptide: Cyclin-dependent kinase 1
    • Protein or peptide: G2/mitotic-specific cyclin-B1,G2/mitotic-specific cyclin-B1
    • Protein or peptide: Cyclin-dependent kinases regulatory subunit 1
  • Ligand: PHOSPHATE ION
Keywordsautoinhibition phosphate-binding pocket pseudosubstrate Scc1 / HYDROLASE
Function / homology
Function and homology information


regulation of Schwann cell differentiation / cyclin A1-CDK1 complex / regulation of attachment of mitotic spindle microtubules to kinetochore / pronuclear fusion / negative regulation of sister chromatid cohesion / response to DDT / cyclin B1-CDK1 complex / separase / positive regulation of mitochondrial ATP synthesis coupled electron transport / Mitotic Prophase ...regulation of Schwann cell differentiation / cyclin A1-CDK1 complex / regulation of attachment of mitotic spindle microtubules to kinetochore / pronuclear fusion / negative regulation of sister chromatid cohesion / response to DDT / cyclin B1-CDK1 complex / separase / positive regulation of mitochondrial ATP synthesis coupled electron transport / Mitotic Prophase / regulation of chromosome condensation / positive regulation of mitotic sister chromatid segregation / histone kinase activity / meiotic chromosome separation / Golgi disassembly / microtubule cytoskeleton organization involved in mitosis / E2F-enabled inhibition of pre-replication complex formation / G2/M DNA replication checkpoint / ventricular cardiac muscle cell development / Depolymerization of the Nuclear Lamina / positive regulation of attachment of spindle microtubules to kinetochore / MASTL Facilitates Mitotic Progression / positive regulation of mRNA 3'-end processing / regulation of mitotic cell cycle spindle assembly checkpoint / mitotic sister chromatid separation / Activation of NIMA Kinases NEK9, NEK6, NEK7 / mitotic nuclear membrane disassembly / homologous chromosome segregation / : / Phosphorylation of Emi1 / patched binding / cyclin A2-CDK1 complex / establishment of mitotic spindle localization / Transcriptional regulation by RUNX2 / Phosphorylation of the APC/C / tissue regeneration / Nuclear Pore Complex (NPC) Disassembly / meiotic spindle organization / outer kinetochore / positive regulation of mitotic metaphase/anaphase transition / protein localization to kinetochore / Transcription of E2F targets under negative control by p107 (RBL1) and p130 (RBL2) in complex with HDAC1 / Initiation of Nuclear Envelope (NE) Reformation / Polo-like kinase mediated events / Golgi Cisternae Pericentriolar Stack Reorganization / cellular response to fatty acid / cyclin-dependent protein serine/threonine kinase activator activity / Condensation of Prometaphase Chromosomes / chromosome condensation / digestive tract development / oocyte maturation / [RNA-polymerase]-subunit kinase / centrosome cycle / cyclin-dependent protein serine/threonine kinase regulator activity / SCF ubiquitin ligase complex / response to copper ion / mitotic metaphase chromosome alignment / MAPK3 (ERK1) activation / response to amine / cyclin-dependent protein kinase activity / G1/S-Specific Transcription / mitotic G2 DNA damage checkpoint signaling / Regulation of APC/C activators between G1/S and early anaphase / microtubule organizing center / ubiquitin-like protein ligase binding / mitotic sister chromatid segregation / mitotic cytokinesis / catalytic activity / regulation of embryonic development / peptidyl-threonine phosphorylation / protein deubiquitination / cysteine-type endopeptidase inhibitor activity / positive regulation of G2/M transition of mitotic cell cycle / chromosome organization / response to cadmium ion / cyclin-dependent kinase / response to mechanical stimulus / cyclin-dependent protein serine/threonine kinase activity / response to axon injury / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / Regulation of MITF-M-dependent genes involved in cell cycle and proliferation / Cyclin A/B1/B2 associated events during G2/M transition / Nuclear events stimulated by ALK signaling in cancer / positive regulation of cardiac muscle cell proliferation / cyclin-dependent protein kinase holoenzyme complex / ERK1 and ERK2 cascade / Hsp70 protein binding / epithelial cell differentiation / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / RNA polymerase II CTD heptapeptide repeat kinase activity / APC/C:Cdc20 mediated degradation of Cyclin B / Recruitment of mitotic centrosome proteins and complexes / cysteine-type peptidase activity / positive regulation of mitotic cell cycle / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / cyclin binding / regulation of mitotic cell cycle / Resolution of Sister Chromatid Cohesion
Similarity search - Function
Securin sister-chromatid separation inhibitor / Securin sister-chromatid separation inhibitor / : / Peptidase C50, separase / SEPARIN core domain / Separin, protease domain / SEPARIN core domain profile. / Cyclin-dependent kinase, regulatory subunit / Cyclin-dependent kinase, regulatory subunit superfamily / Cyclin-dependent kinase regulatory subunit ...Securin sister-chromatid separation inhibitor / Securin sister-chromatid separation inhibitor / : / Peptidase C50, separase / SEPARIN core domain / Separin, protease domain / SEPARIN core domain profile. / Cyclin-dependent kinase, regulatory subunit / Cyclin-dependent kinase, regulatory subunit superfamily / Cyclin-dependent kinase regulatory subunit / Cyclin-dependent kinases regulatory subunits signature 1. / Cyclin-dependent kinases regulatory subunits signature 2. / Cyclin-dependent kinase regulatory subunit / : / Cyclin, C-terminal domain / : / Cyclins signature. / Cyclin / Cyclin, C-terminal domain / Cyclin_C / Cyclin, N-terminal / Cyclin, N-terminal domain / Cyclin-like / domain present in cyclins, TFIIB and Retinoblastoma / Cyclin-like superfamily / : / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Securin / Cyclin-dependent kinase 1 / G2/mitotic-specific cyclin-B1 / Cyclin-dependent kinases regulatory subunit 1 / Separin
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsYu J / Raia P
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-
UpdateNov 13, 2024-
Current statusNov 13, 2024Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.019
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.019
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-7nj0
  • Surface level: 0.019
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_12368.png

Downloads & links

-
Map

FileDownload / File: emd_12368.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSeparase-Cdk1-cyclin B1-Cks1 complex (postprocessed).
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.88 Å/pix.
x 360 pix.
= 316.8 Å		0.88 Å/pix.
x 360 pix.
= 316.8 Å		0.88 Å/pix.
x 360 pix.
= 316.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.88 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.019 / Movie #1: 0.019
Minimum - Maximum-0.05663432 - 0.08854465
Average (Standard dev.)0.000081366925 (±0.0017409691)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 316.8 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.880.880.88
M x/y/z360360360
origin x/y/z0.0000.0000.000
length x/y/z316.800316.800316.800
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ450450450
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS360360360
D min/max/mean-0.0570.0890.000

-
Supplemental data

-
Additional map: Separase-Cdk1-cyclin B1-Cks1 complex (unsharpened).

Fileemd_12368_additional_1.map
AnnotationSeparase-Cdk1-cyclin B1-Cks1 complex (unsharpened).
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Mutual inhibitory complex of human separase-Cdk1-cyclin B1-Cks1 (...

EntireName: Mutual inhibitory complex of human separase-Cdk1-cyclin B1-Cks1 (CCC) complex.
Components
  • Complex: Mutual inhibitory complex of human separase-Cdk1-cyclin B1-Cks1 (CCC) complex.
    • Protein or peptide: Securin,Separin
    • Protein or peptide: Cyclin-dependent kinase 1
    • Protein or peptide: G2/mitotic-specific cyclin-B1,G2/mitotic-specific cyclin-B1
    • Protein or peptide: Cyclin-dependent kinases regulatory subunit 1
  • Ligand: PHOSPHATE ION

-
Supramolecule #1: Mutual inhibitory complex of human separase-Cdk1-cyclin B1-Cks1 (...

SupramoleculeName: Mutual inhibitory complex of human separase-Cdk1-cyclin B1-Cks1 (CCC) complex.
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Homo sapiens (human)

-
Macromolecule #1: Securin,Separin

MacromoleculeName: Securin,Separin / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: separase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 244.677328 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MQLGPPSPVK MPSPPWESNL LQSPSSILST LDVELPPVCC DIDIGGSGGS GGGSGGGSGE NLYFQGGGSG GSGMRSFKRV NFGTLLSSQ KEAEELLPDL KEFLSNPPAG FPSSRSDAER RQACDAILRA CNQQLTAKLA CPRHLGSLLE LAELACDGYL V STPQRPPL ...String:
MQLGPPSPVK MPSPPWESNL LQSPSSILST LDVELPPVCC DIDIGGSGGS GGGSGGGSGE NLYFQGGGSG GSGMRSFKRV NFGTLLSSQ KEAEELLPDL KEFLSNPPAG FPSSRSDAER RQACDAILRA CNQQLTAKLA CPRHLGSLLE LAELACDGYL V STPQRPPL YLERILFVLL RNAAAQGSPE VTLRLAQPLH ACLVQCSREA APQDYEAVAR GSFSLLWKGA EALLERRAAF AA RLKALSF LVLLEDESTP CEVPHFASPT ACRAVAAHQL FDASGHGLNE ADADFLDDLL SRHVIRALVG ERGSSSGLLS PQR ALCLLE LTLEHCRRFC WSRHHDKAIS AVEKAHSYLR NTNLAPSLQL CQLGVKLLQV GEEGPQAVAK LLIKASAVLS KSME APSPP LRALYESCQF FLSGLERGTK RRYRLDAILS LFAFLGGYCS LLQQLRDDGV YGGSSKQQQS FLQMYFQGLH LYTVV VYDF AQGCQIVDLA DLTQLVDSCK STVVWMLEAL EGLSGQELTD HMGMTASYTS NLAYSFYSHK LYAEACAISE PLCQHL GLV KPGTYPEVPP EKLHRCFRLQ VESLKKLGKQ AQGCKMVILW LAALQPCSPE HMAEPVTFWV RVKMDAARAG DKELQLK TL RDSLSGWDPE TLALLLREEL QAYKAVRADT GQERFNIICD LLELSPEETP AGAWARATHL VELAQVLCYH DFTQQTNC S ALDAIREALQ LLDSVRPEAQ ARDQLLDDKA QALLWLYICT LEAKIQEGIE RDRRAQAPGN LEEFEVNDLN YEDKLQEDR FLYSNIAFNL AADAAQSKCL DQALALWKEL LTKGQAPAVR CLQQTAASLQ ILAALYQLVA KPMQALEVLL LLRIVSERLK DHSKAAGSS CHITQLLLTL GCPSYAQLHL EEAASSLKHL DQTTDTYLLL SLTCDLLRSQ LYWTHQKVTK GVSLLLSVLR D PALQKSSK AWYLLRVQVL QLVAAYLSLP SNNLSHSLWE QLCAQGWQTP EIALIDSHKL LRSIILLLMG SDILSTQKAA VE TSFLDYG ENLVQKWQVL SEVLSCSEKL VCHLGRLGSV SEAKAFCLEA LKLTTKLQIP RQCALFLVLK GELELARNDI DLC QSDLQQ VLFLLESCTE FGGVTQHLDS VKKVHLQKGK QQAQVPCPPQ LPEEELFLRG PALELVATVA KEPGPIAPST NS (SEP)PVLKTK PQPIPNFLSH SPTCDCSLCA SPVLTAVCLR WVLVTAGVRL AMGHQAQGLD LLQVVLKGCP EAAERLTQA LQASLNHKTP PSLVPSLLDE ILAQAYTLLA LEGLNQPSNE SLQKVLQSGL KFVAARIPHL EPWRASLLLI WALTKLGGLS CCTTQLFAS SWGWQPPLIK SVPGSEPSKT QGQKRSGRGR QKLASAPLSL NNTSQKGLEG RGLPCTPKPP DRIRQAGPHV P FTVFEEVC PTESKPEVPQ APRVQQRVQT RLKVNFSDDS DLEDPVSAEA WLAEEPKRRG TASRGRGRAR KGLSLKTDAV VA PGSAPGN PGLNGRSRRA KKVASRHCEE RRPQRASDQA RPGPEIMRTI PEEELTDNWR KMSFEILRGS DGEDSASGGK TPA PGPEAA SGEWELLRLD SSKKKLPSPC PDKESDKDLG PRLQLPSAPV ATGLSTLDSI CDSLSVAFRG ISHCPPSGLY AHLC RFLAL CLGHRDPYAT AFLVTESVSI TCRHQLLTHL HRQLSKAQKH RGSLEIADQL QGLSLQEMPG DVPLARIQRL FSFRA LESG HFPQPEKESF QERLALIPSG VTVCVLALAT LQPGTVGNTL LLTRLEKDSP PVSVQIPTGQ NKLHLRSVLN EFDAIQ KAQ KENSSCTDKR EWWTGRLALD HRMEVLIASL EKSVLGCWKG LLLPSSEEPG PAQEASRLQE LLQDCGWKYP DRTLLKI ML SGAGALTPQD IQALAYGLCP TQPERAQELL NEAVGRLQGL TVPSNSHLVL VLDKDLQKLP WESMPSLQAL PVTRLPSF R FLLSYSIIKE YGASPVLSQG VDPRSTFYVL NPHNNLSSTE EQFRANFSSE AGWRGVVGEV PRPEQVQEAL TKHDLYIYA GHGAGARFLD GQAVLRLSCR AVALLFGSSS AALAVHGNLE GAGIVLKYIM AGCPLFLGNL WDVTDRDIDR YTEALLQGWL GAGPGAPLL YYVNQARQAP RLKYLIGAAP IAYGLPVSLR SSLAEENLYF QSWSHPQFEK GGGSGGGSGG GSWSHPQFEK

UniProtKB: Securin, Separin

-
Macromolecule #2: Cyclin-dependent kinase 1

MacromoleculeName: Cyclin-dependent kinase 1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: cyclin-dependent kinase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 36.667098 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MEDYTKIEKI GEGTYGVVYK GRHKTTGQVV AMKKIRLESE EEGVPSTAIR EISLLKELRH PNIVSLQDVL MQDSRLYLIF EFLSMDLKK YLDSIPPGQY MDSSLVKSYL YQILQGIVFC HSRRVLHRDL KPQNLLIDDK GTIKLADFGL ARAFGIPIRV Y (TPO)HEVVTLW ...String:
MEDYTKIEKI GEGTYGVVYK GRHKTTGQVV AMKKIRLESE EEGVPSTAIR EISLLKELRH PNIVSLQDVL MQDSRLYLIF EFLSMDLKK YLDSIPPGQY MDSSLVKSYL YQILQGIVFC HSRRVLHRDL KPQNLLIDDK GTIKLADFGL ARAFGIPIRV Y (TPO)HEVVTLW YRSPEVLLGS ARYSTPVDIW SIGTIFAELA TKKPLFHGDS EIDQLFRIFR ALGTPNNEVW PEVESLQD Y KNTFPKWKPG SLASHVKNLD ENGLDLLSKM LIYDPAKRIS GKMALNHPYF NDLDNQIKKM IAAEALEVLF QGPHHHHHH HH

UniProtKB: Cyclin-dependent kinase 1

-
Macromolecule #3: G2/mitotic-specific cyclin-B1,G2/mitotic-specific cyclin-B1

MacromoleculeName: G2/mitotic-specific cyclin-B1,G2/mitotic-specific cyclin-B1
type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 52.625723 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MALRVTRNSK INAENKAKIN MAGAKRVPTA PAATSKPGLR PRTALGDIGN KVSEQLQAKM PMKKEAKPSA TGKVIDKKLP KPLEKVPML VPVPVSEPVP EPEPEPEPEP VKEEKLSPEP ILVDTASPSP METSGCAPAE EDLCQAFSDV ILAVNDVDAE D GADPNLCS ...String:
MALRVTRNSK INAENKAKIN MAGAKRVPTA PAATSKPGLR PRTALGDIGN KVSEQLQAKM PMKKEAKPSA TGKVIDKKLP KPLEKVPML VPVPVSEPVP EPEPEPEPEP VKEEKLSPEP ILVDTASPSP METSGCAPAE EDLCQAFSDV ILAVNDVDAE D GADPNLCS EYVKDIYAYL RQLEEEQAVR PKYLLGREVT GNMRAILIDW LVQVQMKFRL LQETMYMTVS IIDRFMQNNC VP KKMLQLV GVTAMFIASK YEEMYPPEIG DFAFVTDNTY TKHQIRQMEM KILRALNFGL GRPLPLHFLR RASKIGEVDV EQH TLAKYL MELTMLDYDM VHFPPSQIAA GAFCLALKIL DNGEWTPTLQ HYLSYTEESL LPVMQHLAKN VVMVNQGLTK HMTV KNKYA TSKHAKISTL PQLNSALVQD LAKAVAKVSS LAEENLYFQS WSHPQFEKGG GSGGGSGGGS WSHPQFEK

UniProtKB: G2/mitotic-specific cyclin-B1

-
Macromolecule #4: Cyclin-dependent kinases regulatory subunit 1

MacromoleculeName: Cyclin-dependent kinases regulatory subunit 1 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 9.679211 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString:
MSHKQIYYSD KYDDEEFEYR HVMLPKDIAK LVPKTHLMSE SEWRNLGVQQ SQGWVHYMIH EPEPHILLFR RPLPKKPKK

UniProtKB: Cyclin-dependent kinases regulatory subunit 1

-
Macromolecule #5: PHOSPHATE ION

MacromoleculeName: PHOSPHATE ION / type: ligand / ID: 5 / Number of copies: 1 / Formula: PO4
Molecular weightTheoretical: 94.971 Da
Chemical component information

ChemComp-PO4:
PHOSPHATE ION

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.050 mg/mL
BufferpH: 7.8
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / 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
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 5 / Number real images: 13640 / Average exposure time: 3.0 sec. / Average electron dose: 78.0 e/Å2
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 FIELD / 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
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 312836
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

-
Atomic model buiding 1

Initial model
PDB IDChain

1qmz

source_name: PDB, initial_model_type: experimental model

4yc3

source_name: PDB, initial_model_type: experimental model
RefinementProtocol: AB INITIO MODEL
Output model

PDB-7nj0:
CryoEM structure of the human Separase-Cdk1-cyclin B1-Cks1 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