[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 IONPhosphate
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
Securin sister-chromatid separation inhibitor / Securin sister-chromatid separation inhibitor / Peptidase C50, separase / SEPARIN core 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. ...Securin sister-chromatid separation inhibitor / Securin sister-chromatid separation inhibitor / Peptidase C50, separase / SEPARIN core 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 / 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: 0.019
  • 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).
Voxel sizeX=Y=Z: 0.88 Å
Density
Contour LevelBy AUTHOR: 0.019 / Movie #1: 0.019
Minimum - Maximum-0.05663432 - 0.08854465
Average (Standard dev.)8.1366925e-05 (±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 IONPhosphate

-
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)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)

-
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

-
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

-
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

-
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

-
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 / Phosphate

-
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
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: 5 / Number real images: 13640 / Average exposure time: 3.0 sec. / Average electron dose: 78.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

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

-
Atomic model buiding 1

Initial model(PDB ID:

1qmz

,

4yc3

)
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