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- EMDB-52306: Cryo-EM structure of human separase bound to phosphorylated SCC1 ... -

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Basic information

Entry
Database: EMDB / ID: EMD-52306
TitleCryo-EM structure of human separase bound to phosphorylated SCC1 (310-550 aa)
Map dataPostprocessed map of human separase bound to phosphorylated SCC1 (310-550 aa)
Sample
  • Complex: Human separase bound to phosphorylated SCC1 (310-550 aa)
    • Protein or peptide: Double-strand-break repair protein rad21 homolog
    • Protein or peptide: Separin
  • Ligand: ZINC ION
KeywordsSeparase / cell cycle / SCC1 / RAD21 / protease / chromosome segregation / Auto-cleavage / cohesin
Function / homology
Function and homology information


negative regulation of sister chromatid cohesion / separase / meiotic chromosome separation / negative regulation of mitotic metaphase/anaphase transition / Cohesin Loading onto Chromatin / meiotic cohesin complex / Establishment of Sister Chromatid Cohesion / establishment of meiotic sister chromatid cohesion / cohesin complex / mitotic cohesin complex ...negative regulation of sister chromatid cohesion / separase / meiotic chromosome separation / negative regulation of mitotic metaphase/anaphase transition / Cohesin Loading onto Chromatin / meiotic cohesin complex / Establishment of Sister Chromatid Cohesion / establishment of meiotic sister chromatid cohesion / cohesin complex / mitotic cohesin complex / positive regulation of sister chromatid cohesion / mitotic sister chromatid separation / homologous chromosome segregation / negative regulation of glial cell apoptotic process / establishment of mitotic spindle localization / negative regulation of G2/M transition of mitotic cell cycle / meiotic spindle organization / replication-born double-strand break repair via sister chromatid exchange / positive regulation of mitotic metaphase/anaphase transition / establishment of mitotic sister chromatid cohesion / chromatin looping / reciprocal meiotic recombination / sister chromatid cohesion / negative regulation of interleukin-1 beta production / lncRNA binding / mitotic sister chromatid segregation / mitotic cytokinesis / positive regulation of interleukin-10 production / catalytic activity / negative regulation of tumor necrosis factor production / chromosome, centromeric region / SUMOylation of DNA damage response and repair proteins / cis-regulatory region sequence-specific DNA binding / protein localization to chromatin / cysteine-type peptidase activity / Meiotic synapsis / Resolution of Sister Chromatid Cohesion / condensed nuclear chromosome / chromosome segregation / nuclear matrix / spindle pole / mitotic spindle / Separation of Sister Chromatids / double-strand break repair / chromosome / midbody / DNA recombination / Estrogen-dependent gene expression / DNA-binding transcription factor binding / negative regulation of neuron apoptotic process / response to hypoxia / cell division / cysteine-type endopeptidase activity / apoptotic process / centrosome / chromatin binding / regulation of transcription by RNA polymerase II / chromatin / proteolysis / nucleoplasm / nucleus / membrane / cytosol / cytoplasm
Similarity search - Function
Peptidase C50, separase / SEPARIN core domain / Separin, protease domain / SEPARIN core domain profile. / : / Rad21/Rec8-like protein, C-terminal, eukaryotic / Rad21/Rec8-like protein, N-terminal / Rad21/Rec8-like protein / Conserved region of Rad21 / Rec8 like protein / N terminus of Rad21 / Rec8 like protein ...Peptidase C50, separase / SEPARIN core domain / Separin, protease domain / SEPARIN core domain profile. / : / Rad21/Rec8-like protein, C-terminal, eukaryotic / Rad21/Rec8-like protein, N-terminal / Rad21/Rec8-like protein / Conserved region of Rad21 / Rec8 like protein / N terminus of Rad21 / Rec8 like protein / ScpA-like, C-terminal / Winged helix DNA-binding domain superfamily
Similarity search - Domain/homology
Double-strand-break repair protein rad21 homolog / Separin
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.93 Å
AuthorsYu J / Schmidt S / Botto M / Boland A
Funding support Switzerland, 2 items
OrganizationGrant numberCountry
Swiss National Science Foundation310030_185235 Switzerland
Swiss National Science FoundationTMSGI3_211581 Switzerland
CitationJournal: To Be Published
Title: Structural insights into cohesin cleavage by human separase
Authors: Yu J / Schmidt S / Botto M / Ghent CM / Morgan DO / Boland A
History
DepositionDec 10, 2024-
Header (metadata) releaseSep 3, 2025-
Map releaseSep 3, 2025-
UpdateSep 3, 2025-
Current statusSep 3, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_52306.png

Downloads & links

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Map

FileDownload / File: emd_52306.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPostprocessed map of human separase bound to phosphorylated SCC1 (310-550 aa)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.9 Å/pix.
x 400 pix.
= 360.96 Å		0.9 Å/pix.
x 400 pix.
= 360.96 Å		0.9 Å/pix.
x 400 pix.
= 360.96 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.9024 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 3.0
Minimum - Maximum-0.24892184 - 20.077583000000001
Average (Standard dev.)-0.020232955 (±0.33833924)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 360.96002 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Unsharpened map of human separase bound to phosphorylated...

Fileemd_52306_additional_1.map
AnnotationUnsharpened map of human separase bound to phosphorylated SCC1 (310-550 aa)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Focus-refined map 1 (postprocessed) of human separase bound...

Fileemd_52306_additional_2.map
AnnotationFocus-refined map 1 (postprocessed) of human separase bound to phosphorylated SCC1 (310-550 aa)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Focus-refined map 2 (postprocessed) of human separase bound...

Fileemd_52306_additional_3.map
AnnotationFocus-refined map 2 (postprocessed) of human separase bound to phosphorylated SCC1 (310-550 aa)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A of human separase bound to...

Fileemd_52306_half_map_1.map
AnnotationHalf map A of human separase bound to phosphorylated SCC1 (310-550 aa)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B of human separase bound to...

Fileemd_52306_half_map_2.map
AnnotationHalf map B of human separase bound to phosphorylated SCC1 (310-550 aa)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Human separase bound to phosphorylated SCC1 (310-550 aa)

EntireName: Human separase bound to phosphorylated SCC1 (310-550 aa)
Components
  • Complex: Human separase bound to phosphorylated SCC1 (310-550 aa)
    • Protein or peptide: Double-strand-break repair protein rad21 homolog
    • Protein or peptide: Separin
  • Ligand: ZINC ION

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Supramolecule #1: Human separase bound to phosphorylated SCC1 (310-550 aa)

SupramoleculeName: Human separase bound to phosphorylated SCC1 (310-550 aa)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 262 KDa

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Macromolecule #1: Double-strand-break repair protein rad21 homolog

MacromoleculeName: Double-strand-break repair protein rad21 homolog / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 27.773189 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: DITVKETKAK RKRKLIVDSV KELDSKTIRA QLSDYSDIVT TLDLAPPTKK LMMWKETGGV EKLFSLPAQP LWNNRLLKLF TRCLTPLVP EDLRKRRKGG EADNLDEFLK EFENPEVPRE DQQQQHQQRD VIDEPIIEEP SRLQE(SEP)VMEA SRTNIDE SA MPPPPPQGVK ...String:
DITVKETKAK RKRKLIVDSV KELDSKTIRA QLSDYSDIVT TLDLAPPTKK LMMWKETGGV EKLFSLPAQP LWNNRLLKLF TRCLTPLVP EDLRKRRKGG EADNLDEFLK EFENPEVPRE DQQQQHQQRD VIDEPIIEEP SRLQE(SEP)VMEA SRTNIDE SA MPPPPPQGVK RKAGQIDPEP VMPPQQVEQM EIPPVELPPE EPPNICQLIP ELELLPEKEK EKEKEKEDDE EEEDEDAS G GDQD

UniProtKB: Double-strand-break repair protein rad21 homolog

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Macromolecule #2: Separin

MacromoleculeName: Separin / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: separase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 238.086344 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MDYKDHDGDY KDHDIDYKDD DDKSGPGGSG GSGGGSGGGS GENLYFQGGG SGGSGMRSFK RVNFGTLLSS QKEAEELLPD LKEFLSNPP AGFPSSRSDA ERRQACDAIL RACNQQLTAK LACPRHLGSL LELAELACDG YLVSTPQRPP LYLERILFVL L RNAAAQGS ...String:
MDYKDHDGDY KDHDIDYKDD DDKSGPGGSG GSGGGSGGGS GENLYFQGGG SGGSGMRSFK RVNFGTLLSS QKEAEELLPD LKEFLSNPP AGFPSSRSDA ERRQACDAIL RACNQQLTAK LACPRHLGSL LELAELACDG YLVSTPQRPP LYLERILFVL L RNAAAQGS PEVTLRLAQP LHACLVQCSR EAAPQDYEAV ARGSFSLLWK GAEALLERRA AFAARLKALS FLVLLEDEST PC EVPHFAS PTACRAVAAH QLFDASGHGL NEADADFLDD LLSRHVIRAL VGERGSSSGL LSPQRALCLL ELTLEHCRRF CWS RHHDKA ISAVEKAHSY LRNTNLAPSL QLCQLGVKLL QVGEEGPQAV AKLLIKASAV LSKSMEAPSP PLRALYESCQ FFLS GLERG TKRRYRLDAI LSLFAFLGGY CSLLQQLRDD GVYGGSSKQQ QSFLQMYFQG LHLYTVVVYD FAQGCQIVDL ADLTQ LVDS CKSTVVWMLE ALEGLSGQEL TDHMGMTASY TSNLAYSFYS HKLYAEACAI SEPLCQHLGL VKPGTYPEVP PEKLHR CFR LQVESLKKLG KQAQGCKMVI LWLAALQPCS PEHMAEPVTF WVRVKMDAAR AGDKELQLKT LRDSLSGWDP ETLALLL RE ELQAYKAVRA DTGQERFNII CDLLELSPEE TPAGAWARAT HLVELAQVLC YHDFTQQTNC SALDAIREAL QLLDSVRP E AQARDQLLDD KAQALLWLYI CTLEAKMQEG IERDRRAQAP GNLEEFEVND LNYEDKLQED RFLYSNIAFN LAADAAQSK CLDQALALWK ELLTKGQAPA VRCLQQTAAS LQILAALYQL VAKPMQALEV LLLLRIVSER LKDHSKAAGS SCHITQLLLT LGCPSYAQL HLEEAASSLK HLDQTTDTYL LLSLTCDLLR SQLYWTHQKV TKGVSLLLSV LRDPALQKSS KAWYLLRVQV L QLVAAYLS LPSNNLSHSL WEQLCAQGWQ TPEIALIDSH KLLRSIILLL MGSDILSTQK AAVETSFLDY GENLVQKWQV LS EVLSCSE KLVCHLGRLG SVSEAKAFCL EALKLTTKLQ IPRQCALFLV LKGELELARN DIDLCQSDLQ QVLFLLESCT EFG GVTQHL DSVKKVHLQK GKQQAQVPCP PQLPEEELFL RGPALELVAT VAKEPGPIAP STNSSPVLKT KPQPIPNFLS HSPT CDCSL CASPVLTAVC LRWVLVTAGV RLAMGHQAQG LDLLQVVLKG CPEAAERLTQ ALQASLNHKT PPSLVPSLLD EILAQ AYTL LALEGLNQPS NESLQKVLQS GLKFVAARIP HLEPWRASLL LIWALTKLGG LSCCTTQLFA SSWGWQPPLI KSVPGS EPS KTQGQKRSGR GRQKLASAPL SLNNTSQKGL EGRGLPCTPK PPDRIRQAGP HVPFTVFEEV CPTESKPEVP QAPRVQQ RV QTRLKVNFSD DSDLEDPVSA EAWLAEEPKR RGTASRGRGR ARKGLSLKTD AVVAPGSAPG NPGLNGRSRR AKKVASRH C EERRPQRASD QARPGGLEVL FQGPGSGDSS KKKLPSPCPD KESDKDLGPR LQLPSAPVAT GLSTLDSICD SLSVAFRGI SHCPPSGLYA HLCRFLALCL GHRDPYATAF LVTESVSITC RHQLLTHLHR QLSKAQKHRG SLEIADQLQG LSLQEMPGDV PLARIQRLF SFRALESGHF PQPEKESFQE RLALIPSGVT VCVLALATLQ PGTVGNTLLL TRLEKDSPPV SVQIPTGQNK L HLRSVLNE FDAIQKAQKE NSSCTDKREW WTGRLALDHR MEVLIASLEK SVLGCWKGLL LPSSEEPGPA QEASRLQELL QD CGWKYPD RTLLKIMLSG AGALTPQDIQ ALAYGLCPTQ PERAQELLNE AVGRLQGLTV PSNSHLVLVL DKDLQKLPWE SMP SLQALP VTRLPSFRFL LSYSIIKEYG ASPVLSQGVD PRSTFYVLNP HNNLSSTEEQ FRANFSSEAG WRGVVGEVPR PEQV QEALT KHDLYIYAGH GAGARFLDGQ AVLRLSCRAV ALLFGSSSAA LAVHGNLEGA GIVLKYIMAG CPLFLGNLWD VTDRD IDRY TEALLQGWLG AGPGAPLLYY VNQARQAPRL KYLIGAAPIA YGLPVSLRSS LAEENLYFQS WSHPQFEKGG GSGGGS GGG SWSHPQFEK

UniProtKB: Separin, Separin

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Macromolecule #3: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 3 / Number of copies: 1 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.06 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
20.0 mMHepes2-[4-(2-hydroxyethyl)piperazin-1-yl]ethanesulfonic acid
80.0 mMKClPotassium chloride
0.5 mMTCEPtris(2-carboxyethyl)phosphine
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GRAPHENE OXIDE / Support film - topology: CONTINUOUS / Support film - Film thickness: 1 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 277.15 K / Instrument: LEICA EM GP

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Specialist opticsEnergy filter - Name: TFS Selectris X / Energy filter - Slit width: 10 eV
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number grids imaged: 2 / Number real images: 7451 / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 130000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 6692171 / Details: The particles were automatically selected
CTF correctionSoftware - Name: cryoSPARC (ver. 4.4.0) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionNumber classes used: 1 / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.93 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.4.0) / Software - details: Non-uniform refinement was used / Number images used: 298574
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.4.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.4.0)
Final 3D classificationNumber classes: 4 / Software - Name: cryoSPARC (ver. 4.4.0)

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Atomic model buiding 1

Initial modelPDB ID:

7nj1


Chain - Chain ID: A / Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-9hn4:
Cryo-EM structure of human separase bound to phosphorylated SCC1 (310-550 aa)

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