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- EMDB-52298: Cryo-EM structure of SA2-SCC1 complex at 2.9 angstrom -

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Basic information

Entry
Database: EMDB / ID: EMD-52298
TitleCryo-EM structure of SA2-SCC1 complex at 2.9 angstrom
Map dataPostprocessed map of SA2-SCC1 complex
Sample
  • Complex: SA2-SCC1 complex
    • Protein or peptide: Cohesin subunit SA-2
    • Protein or peptide: Double-strand-break repair protein rad21 homolog
KeywordsSeparase / cell cycle / SCC1 / RAD21 / protease / chromosome segregation / Auto-cleavage / SA1/2 / cohesin
Function / homology
Function and homology information


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 / negative regulation of glial cell apoptotic process / negative regulation of G2/M transition of mitotic cell cycle ...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 / negative regulation of glial cell apoptotic process / negative regulation of G2/M transition of mitotic cell cycle / replication-born double-strand break repair via sister chromatid exchange / establishment of mitotic sister chromatid cohesion / chromatin looping / reciprocal meiotic recombination / sister chromatid cohesion / negative regulation of interleukin-1 beta production / mitotic spindle pole / lncRNA binding / positive regulation of interleukin-10 production / negative regulation of tumor necrosis factor production / chromosome, centromeric region / mitotic spindle assembly / SUMOylation of DNA damage response and repair proteins / cis-regulatory region sequence-specific DNA binding / protein localization to chromatin / Meiotic synapsis / Resolution of Sister Chromatid Cohesion / condensed nuclear chromosome / meiotic cell cycle / chromosome segregation / nuclear matrix / fibrillar center / spindle pole / Separation of Sister Chromatids / double-strand break repair / chromosome / midbody / DNA recombination / DNA-binding transcription factor binding / Estrogen-dependent gene expression / negative regulation of neuron apoptotic process / response to hypoxia / cell division / apoptotic process / chromatin binding / regulation of transcription by RNA polymerase II / chromatin / nucleolus / nucleoplasm / nucleus / membrane / cytosol
Similarity search - Function
: / Cohesin subunit SCC3/SA, HEAT-repeats domain / STAG / Stromalin conservative domain / Cohesin subunit Scc3/SA / STAG domain / Stromalin conservative domain / Stromalin conservative (SCD) domain profile. / : / Rad21/Rec8-like protein, C-terminal, eukaryotic ...: / Cohesin subunit SCC3/SA, HEAT-repeats domain / STAG / Stromalin conservative domain / Cohesin subunit Scc3/SA / STAG domain / Stromalin conservative domain / Stromalin conservative (SCD) 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 / Armadillo-type fold / Winged helix DNA-binding domain superfamily
Similarity search - Domain/homology
Double-strand-break repair protein rad21 homolog / Cohesin subunit SA-2
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 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 9, 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_52298.png

Downloads & links

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Map

FileDownload / File: emd_52298.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPostprocessed map of SA2-SCC1 complex
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: 4.5
Minimum - Maximum-0.82621217 - 24.758358000000001
Average (Standard dev.)-0.024134347 (±0.31111953)
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 SA2-SCC1 complex

Fileemd_52298_additional_1.map
AnnotationUnsharpened map of SA2-SCC1 complex
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Focus-refined map (mask 4) of SA2-SCC1 complex

Fileemd_52298_additional_2.map
AnnotationFocus-refined map (mask 4) of SA2-SCC1 complex
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Focus-refined map (mask 3) of SA2-SCC1 complex

Fileemd_52298_additional_3.map
AnnotationFocus-refined map (mask 3) of SA2-SCC1 complex
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Composite map (postprocessed) of SA2-SCC1 complex

Fileemd_52298_additional_4.map
AnnotationComposite map (postprocessed) of SA2-SCC1 complex
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A of SA2-SCC1 complex

Fileemd_52298_half_map_1.map
AnnotationHalf map A of SA2-SCC1 complex
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B of SA2-SCC1 complex

Fileemd_52298_half_map_2.map
AnnotationHalf map B of SA2-SCC1 complex
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : SA2-SCC1 complex

EntireName: SA2-SCC1 complex
Components
  • Complex: SA2-SCC1 complex
    • Protein or peptide: Cohesin subunit SA-2
    • Protein or peptide: Double-strand-break repair protein rad21 homolog

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Supramolecule #1: SA2-SCC1 complex

SupramoleculeName: SA2-SCC1 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 130 KDa

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Macromolecule #1: Cohesin subunit SA-2

MacromoleculeName: Cohesin subunit SA-2 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 145.730422 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MIAAPEIPTD FNLLQESETH FSSDTDFEDI EGKNQKQGKG KTCKKGKKGP AEKGKGGNGG GKPPSGPNRM NGHHQQNGVE NMMLFEVVK MGKSAMQSVV DDWIESYKHD RDIALLDLIN FFIQCSGCKG VVTAEMFRHM QNSEIIRKMT EEFDEDSGDY P LTMAGPQW ...String:
MIAAPEIPTD FNLLQESETH FSSDTDFEDI EGKNQKQGKG KTCKKGKKGP AEKGKGGNGG GKPPSGPNRM NGHHQQNGVE NMMLFEVVK MGKSAMQSVV DDWIESYKHD RDIALLDLIN FFIQCSGCKG VVTAEMFRHM QNSEIIRKMT EEFDEDSGDY P LTMAGPQW KKFKSSFCEF IGVLVRQCQY SIIYDEYMMD TVISLLTGLS DSQVRAFRHT STLAAMKLMT ALVNVALNLS IN MDNTQRQ YEAERNKMIG KRANERLELL LQKRKELQEN QDEIENMMNA IFKGVFVHRY RDAIAEIRAI CIEEIGIWMK MYS DAFLND SYLKYVGWTM HDKQGEVRLK CLTALQGLYY NKELNSKLEL FTSRFKDRIV SMTLDKEYDV AVQAIKLLTL VLQS SEEVL TAEDCENVYH LVYSAHRPVA VAAGEFLYKK LFSRRDPEED GMMKRRGRQG PNANLVKTLV FFFLESELHE HAAYL VDSM WDCATELLKD WECMNSLLLE EPLSGEEALT DRQESALIEI MLCTIRQAAE CHPPVGRGTG KRVLTAKEKK TQLDDR TKI TELFAVALPQ LLAKYSVDAE KVTNLLQLPQ YFDLEIYTTG RLEKHLDALL RQIRNIVEKH TDTDVLEACS KTYHALC NE EFTIFNRVDI SRSQLIDELA DKFNRLLEDF LQEGEEPDED DAYQVLSTLK RITAFHNAHD LSKWDLFACN YKLLKTGI E NGDMPEQIVI HALQCTHYVI LWQLAKITES SSTKEDLLRL KKQMRVFCQI CQHYLTNVNT TVKEQAFTIL CDILMIFSH QIMSGGRDML EPLVYTPDSS LQSELLSFIL DHVFIEQDDD NNSADGQQED EASKIEALHK RRNLLAAFCK LIVYTVVEMN TAADIFKQY MKYYNDYGDI IKETMSKTRQ IDKIQCAKTL ILSLQQLFNE MIQENGYNFD RSSSTFSGIK ELARRFALTF G LDQLKTRE AIAMLHKDGI EFAFKEPNPQ GESHPPLNLA FLDILSEFSS KLLRQDKRTV YVYLEKFMTF QMSLRREDVW LP LMSYRNS LLAGGDDDTM SVISGISSRG STVRSKKSKP STGKRKVVEG MQLSLTEESS SSDSMWLSRE QTLHTPVMMQ TPQ LTSTIM REPKRLRPED SFMSVYPMQT EHHQTPLDYN RRGTSLMEDD EEPIVEDVMM SSEGRIEDLN EGMDFDTMDI DLPP SKNRR ERTELKPDFF DPASIMDESV LGVSMFSSLA EENLYFQSWS HPQFEKGGGS GGGSGGGSWS HPQFEK

UniProtKB: Cohesin subunit SA-2

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Macromolecule #2: Double-strand-break repair protein rad21 homolog

MacromoleculeName: Double-strand-break repair protein rad21 homolog / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 27.693211 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: DITVKETKAK RKRKLIVDSV KELDSKTIRA QLSDYSDIVT TLDLAPPTKK LMMWKETGGV EKLFSLPAQP LWNNRLLKLF TRCLTPLVP EDLRKRRKGG EADNLDEFLK EFENPEVPRE DQQQQHQQRD VIDEPIIEEP SRLQESVMEA SRTNIDESAM P PPPPQGVK ...String:
DITVKETKAK RKRKLIVDSV KELDSKTIRA QLSDYSDIVT TLDLAPPTKK LMMWKETGGV EKLFSLPAQP LWNNRLLKLF TRCLTPLVP EDLRKRRKGG EADNLDEFLK EFENPEVPRE DQQQQHQQRD VIDEPIIEEP SRLQESVMEA SRTNIDESAM P PPPPQGVK RKAGQIDPEP VMPPQQVEQM EIPPVELPPE EPPNICQLIP ELELLPEKEK EKEKEKEDDE EEEDEDASGG DQ D

UniProtKB: Double-strand-break repair protein rad21 homolog

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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

Concentration0.1 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
20.0 mMHepes2-[4-(2-hydroxyethyl)piperazin-1-yl]ethanesulfonic acid
150.0 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: 16 / Number real images: 57012 / 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: 106898589 / 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: 2.9 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: 768540
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: 6 / Software - Name: cryoSPARC (ver. 4.4.0)

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Atomic model buiding 1

Initial modelPDB ID:

4pju


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

PDB-9hmv:
Cryo-EM structure of SA2-SCC1 complex at 2.9 angstrom

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