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- EMDB-52290: Cryo-EM structure of apo human separase -

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Basic information

Entry
Database: EMDB / ID: EMD-52290
TitleCryo-EM structure of apo human separase
Map dataPostprocessed map of apo human separase
Sample
  • Complex: Apo human separase
    • Protein or peptide: Separin
  • Ligand: ZINC ION
KeywordsSeparase / cell cycle / SCC1 / RAD21 / protease / chromosome segregation / Auto-cleavage
Function / homology
Function and homology information


negative regulation of sister chromatid cohesion / separase / meiotic chromosome separation / mitotic sister chromatid separation / homologous chromosome segregation / establishment of mitotic spindle localization / meiotic spindle organization / positive regulation of mitotic metaphase/anaphase transition / mitotic sister chromatid segregation / mitotic cytokinesis ...negative regulation of sister chromatid cohesion / separase / meiotic chromosome separation / mitotic sister chromatid separation / homologous chromosome segregation / establishment of mitotic spindle localization / meiotic spindle organization / positive regulation of mitotic metaphase/anaphase transition / mitotic sister chromatid segregation / mitotic cytokinesis / catalytic activity / cysteine-type peptidase activity / mitotic spindle / Separation of Sister Chromatids / cysteine-type endopeptidase activity / apoptotic process / centrosome / proteolysis / nucleus / cytoplasm / cytosol
Similarity search - Function
Peptidase C50, separase / SEPARIN core domain / Separin, protease domain / SEPARIN core domain profile.
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 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 7, 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_52290.png

Downloads & links

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Map

FileDownload / File: emd_52290.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPostprocessed map of apo human separase
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.98 Å/pix.
x 360 pix.
= 351.324 Å		0.98 Å/pix.
x 360 pix.
= 351.324 Å		0.98 Å/pix.
x 360 pix.
= 351.324 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.9759 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 4.0
Minimum - Maximum-0.11378788 - 14.834173
Average (Standard dev.)-0.017448006 (±0.3185147)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 351.324 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Unsharpened map of apo human separase

Fileemd_52290_additional_1.map
AnnotationUnsharpened map of apo human separase
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Focus-refined map 1 (unsharpened) of apo human separase

Fileemd_52290_additional_2.map
AnnotationFocus-refined map 1 (unsharpened) of apo human separase
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Focus-refined map 2 (unsharpened) of apo human separase

Fileemd_52290_additional_3.map
AnnotationFocus-refined map 2 (unsharpened) of apo human separase
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Composite map of apo human separase

Fileemd_52290_additional_4.map
AnnotationComposite map of apo human separase
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A of apo human separase

Fileemd_52290_half_map_1.map
AnnotationHalf map A of apo human separase
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B of apo human separase

Fileemd_52290_half_map_2.map
AnnotationHalf map B of apo human separase
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Apo human separase

EntireName: Apo human separase
Components
  • Complex: Apo human separase
    • Protein or peptide: Separin
  • Ligand: ZINC ION

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Supramolecule #1: Apo human separase

SupramoleculeName: Apo human separase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 230 KDa

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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: 243.151125 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MSGDYKDHDG DYKDHDIDYK DDDDKSGPGG SGGSGGGSGG GSGENLYFQG GGSGGSGMRS FKRVNFGTLL SSQKEAEELL PDLKEFLSN PPAGFPSSRS DAERRQACDA ILRACNQQLT AKLACPRHLG SLLELAELAC DGYLVSTPQR PPLYLERILF V LLRNAAAQ ...String:
MSGDYKDHDG DYKDHDIDYK DDDDKSGPGG SGGSGGGSGG GSGENLYFQG GGSGGSGMRS FKRVNFGTLL SSQKEAEELL PDLKEFLSN PPAGFPSSRS DAERRQACDA ILRACNQQLT AKLACPRHLG SLLELAELAC DGYLVSTPQR PPLYLERILF V LLRNAAAQ GSPEVTLRLA QPLHACLVQC SREAAPQDYE AVARGSFSLL WKGAEALLER RAAFAARLKA LSFLVLLEDE ST PCEVPHF ASPTACRAVA AHQLFDASGH GLNEADADFL DDLLSRHVIR ALVGERGSSS GLLSPQRALC LLELTLEHCR RFC WSRHHD KAISAVEKAH SYLRNTNLAP SLQLCQLGVK LLQVGEEGPQ AVAKLLIKAS AVLSKSMEAP SPPLRALYES CQFF LSGLE RGTKRRYRLD AILSLFAFLG GYCSLLQQLR DDGVYGGSSK QQQSFLQMYF QGLHLYTVVV YDFAQGCQIV DLADL TQLV DSCKSTVVWM LEALEGLSGQ ELTDHMGMTA SYTSNLAYSF YSHKLYAEAC AISEPLCQHL GLVKPGTYPE VPPEKL HRC FRLQVESLKK LGKQAQGCKM VILWLAALQP CSPEHMAEPV TFWVRVKMDA ARAGDKELQL KTLRDSLSGW DPETLAL LL REELQAYKAV RADTGQERFN IICDLLELSP EETPAGAWAR ATHLVELAQV LCYHDFTQQT NCSALDAIRE ALQLLDSV R PEAQARDQLL DDKAQALLWL YICTLEAKMQ EGIERDRRAQ APGNLEEFEV NDLNYEDKLQ EDRFLYSNIA FNLAADAAQ SKCLDQALAL WKELLTKGQA PAVRCLQQTA ASLQILAALY QLVAKPMQAL EVLLLLRIVS ERLKDHSKAA GSSCHITQLL LTLGCPSYA QLHLEEAASS LKHLDQTTDT YLLLSLTCDL LRSQLYWTHQ KVTKGVSLLL SVLRDPALQK SSKAWYLLRV Q VLQLVAAY LSLPSNNLSH SLWEQLCAQG WQTPEIALID SHKLLRSIIL LLMGSDILST QKAAVETSFL DYGENLVQKW QV LSEVLSC SEKLVCHLGR LGSVSEAKAF CLEALKLTTK LQIPRQCALF LVLKGELELA RNDIDLCQSD LQQVLFLLES CTE FGGVTQ HLDSVKKVHL QKGKQQAQVP CPPQLPEEEL FLRGPALELV ATVAKEPGPI APSTNSSPVL KTKPQPIPNF LSHS PTCDC SLCASPVLTA VCLRWVLVTA GVRLAMGHQA QGLDLLQVVL KGCPEAAERL TQALQASLNH KTPPSLVPSL LDEIL AQAY TLLALEGLNQ PSNESLQKVL QSGLKFVAAR IPHLEPWRAS LLLIWALTKL GGLSCCTTQL FASSWGWQPP LIKSVP GSE PSKTQGQKRS GRGRQKLASA PLSLNNTSQK GLEGRGLPCT PKPPDRIRQA GPHVPFTVFE EVCPTESKPE VPQAPRV QQ RVQTRLKVNF SDDSDLEDPV SAEAWLAEEP KRRGTASRGR GRARKGLSLK TDAVVAPGSA PGNPGLNGRS RRAKKVAS R HCEERRPQRA SDQARPGPEI MRTIPEEELT DNWRKMSFEI LRGSDGEDSA SGGKTPAPGP EAASGEWELL RLDSSKKKL PSPCPDKESD KDLGPRLQLP SAPVATGLST LDSICDSLSV AFRGISHCPP SGLYAHLCRF LALCLGHRDP YATAFLVTES VSITCRHQL LTHLHRQLSK AQKHRGSLEI ADQLQGLSLQ EMPGDVPLAR IQRLFSFRAL ESGHFPQPEK ESFQERLALI P SGVTVCVL ALATLQPGTV GNTLLLTRLE KDSPPVSVQI PTGQNKLHLR SVLNEFDAIQ KAQKENSSCT DKREWWTGRL AL DHRMEVL IASLEKSVLG CWKGLLLPSS EEPGPAQEAS RLQELLQDCG WKYPDRTLLK IMLSGAGALT PQDIQALAYG LCP TQPERA QELLNEAVGR LQGLTVPSNS HLVLVLDKDL QKLPWESMPS LQALPVTRLP SFRFLLSYSI IKEYGASPVL SQGV DPRST FYVLNPHNNL SSTEEQFRAN FSSEAGWRGV VGEVPRPEQV QEALTKHDLY IYAGHGAGAR FLDGQAVLRL SCRAV ALLF GCSSAALAVH GNLEGAGIVL KYIMAGCPLF LGNLWDVTDR DIDRYTEALL QGWLGAGPGA PLLYYVNQAR QAPRLK YLI GAAPIAYGLP VSLRSSLAEE NLYFQSWSHP QFEKGGGSGG GSGGGSWSHP QFEK

UniProtKB: Separin

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Macromolecule #2: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 2 / 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

Concentration0.05 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
20.0 mMHepes2-[4-(2-hydroxyethyl)piperazin-1-yl]ethanesulfonic acid
100.0 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
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number grids imaged: 1 / Number real images: 3314 / Average electron dose: 40.0 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: 2.2 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 150000
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: 4023196 / 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: 3.3 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: 224027
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: 3 / 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-9hma:
Cryo-EM structure of apo human separase

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