9HMS: Human separase

Cryo-EM structure of human separase bound to SCC1 (310-550 aa) and SA2. Determined by electron microscopy at 3.4 Å resolution. Released 3 Sept 2025.

Method
Electron microscopy
Resolution
3.4 Å
Organism
Homo sapiens
Chains
3
Atoms
16,909
Mol. weight
411.58 kDa
Ligands
ZN
Released
3 Sept 2025

Explore 9HMS in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9HMS contains 127 α-helices and 19 β-strands across 3 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 60 helices, 1 β-strand

ElementResiduesLengthSheet
α-helix86-894
α-helix96-10813
α-helix115-1239
α-helix141-1433
α-helix144-1507
α-helix166-18621
α-helix197-20913
α-helix213-2197
α-helix220-2245
α-helix225-24925
α-helix262-28726
α-helix288-2936
α-helix296-2983
α-helix302-31817
α-helix331-3344
α-helix335-3373
α-helix342-35514
α-helix362-37716
α-helix378-3803
β-strand38111
α-helix384-40017
α-helix407-4159
α-helix416-4183
α-helix422-43615
α-helix459-47012
α-helix478-4825
α-helix495-5039
α-helix505-5073
α-helix511-5144
α-helix515-53319
α-helix537-5382
α-helix550-57728
α-helix582-5887
α-helix591-5944
α-helix598-6014
α-helix607-62014
α-helix628-63912
α-helix647-67327
α-helix682-69716
α-helix709-72214
α-helix727-74620
α-helix755-77622
α-helix781-79717
α-helix800-8034
α-helix808-8103
α-helix819-83214
α-helix852-87322
α-helix879-8824
α-helix883-8864
α-helix890-8923
α-helix898-91013
α-helix912-93120
α-helix944-95815
α-helix966-98116
α-helix993-9942
α-helix999-10035
α-helix1004-10096
α-helix1012-102615
α-helix1028-10325
α-helix1036-10383
α-helix1039-104810
Chain B: 8 helices, 2 β-strands
ElementResiduesLengthSheet
α-helix334-3429
β-strand34811
α-helix358-3669
α-helix369-3724
α-helix383-3908
α-helix414-4196
α-helix421-4233
β-strand42612
α-helix447-4493
α-helix451-4533
Chain C: 59 helices, 16 β-strands
ElementResiduesLengthSheet
α-helix578-59417
α-helix600-61314
α-helix619-63618
α-helix642-6454
α-helix649-66012
α-helix670-70233
α-helix731-7344
α-helix740-75718
α-helix763-7642
α-helix769-78517
α-helix789-80517
α-helix809-82618
α-helix829-84214
α-helix851-87020
α-helix874-88613
α-helix888-8914
α-helix895-91218
α-helix921-93010
α-helix935-95319
α-helix975-100127
α-helix1004-102118
α-helix1024-104017
α-helix1044-106118
α-helix1149-11524
α-helix1154-117421
α-helix1179-120628
α-helix1211-12122
α-helix1220-123617
α-helix1242-125514
α-helix1262-127716
α-helix1573-158917
α-helix1594-160815
α-helix1609-16113
α-helix1613-16219
α-helix1626-164116
α-helix1668-167710
α-helix1689-16935
α-helix1694-16996
α-helix1702-17032
β-strand170713
β-strand1708-171474
β-strand1724-173184
β-strand1734-174074
α-helix1750-176718
α-helix1773-179321
α-helix1794-17985
α-helix1808-18092
α-helix1815-18173
α-helix1826-18294
α-helix1846-18483
α-helix1851-186111
α-helix1866-187914
β-strand189113
β-strand1894-189524
β-strand191513
β-strand191715
α-helix1921-193212
α-helix1937-19404
β-strand1948-195256
α-helix1959-19646
α-helix1967-19715
β-strand1975-197956
α-helix1982-19843
α-helix1985-199410
β-strand1997-200156
α-helix2012-20165
β-strand2023-202756
α-helix2046-20494
α-helix2050-20523
β-strand2057-205936
β-strand206512
α-helix2066-208318
α-helix2089-20968
β-strand2111-211226
β-strand211315

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
Cohesin subunit SA-2Aprotein1271Homo sapiensQ8N3U4 (AlphaFold model)
Double-strand-break repair protein rad21 homologBprotein241Homo sapiensO60216 (AlphaFold model)
SeparinCprotein2172Homo sapiensQ14674 (AlphaFold model)
Sequence of entity 1 (A), FASTA
>9HMS_1 Cohesin subunit SA-2 (chains A)
MIAAPEIPTDFNLLQESETHFSSDTDFEDIEGKNQKQGKGKTCKKGKKGPAEKGKGGNGG
GKPPSGPNRMNGHHQQNGVENMMLFEVVKMGKSAMQSVVDDWIESYKHDRDIALLDLINF
FIQCSGCKGVVTAEMFRHMQNSEIIRKMTEEFDEDSGDYPLTMAGPQWKKFKSSFCEFIG
VLVRQCQYSIIYDEYMMDTVISLLTGLSDSQVRAFRHTSTLAAMKLMTALVNVALNLSIN
MDNTQRQYEAERNKMIGKRANERLELLLQKRKELQENQDEIENMMNAIFKGVFVHRYRDA
IAEIRAICIEEIGIWMKMYSDAFLNDSYLKYVGWTMHDKQGEVRLKCLTALQGLYYNKEL
NSKLELFTSRFKDRIVSMTLDKEYDVAVQAIKLLTLVLQSSEEVLTAEDCENVYHLVYSA
HRPVAVAAGEFLYKKLFSRRDPEEDGMMKRRGRQGPNANLVKTLVFFFLESELHEHAAYL
VDSMWDCATELLKDWECMNSLLLEEPLSGEEALTDRQESALIEIMLCTIRQAAECHPPVG
RGTGKRVLTAKEKKTQLDDRTKITELFAVALPQLLAKYSVDAEKVTNLLQLPQYFDLEIY
TTGRLEKHLDALLRQIRNIVEKHTDTDVLEACSKTYHALCNEEFTIFNRVDISRSQLIDE
LADKFNRLLEDFLQEGEEPDEDDAYQVLSTLKRITAFHNAHDLSKWDLFACNYKLLKTGI
ENGDMPEQIVIHALQCTHYVILWQLAKITESSSTKEDLLRLKKQMRVFCQICQHYLTNVN
TTVKEQAFTILCDILMIFSHQIMSGGRDMLEPLVYTPDSSLQSELLSFILDHVFIEQDDD
NNSADGQQEDEASKIEALHKRRNLLAAFCKLIVYTVVEMNTAADIFKQYMKYYNDYGDII
KETMSKTRQIDKIQCAKTLILSLQQLFNEMIQENGYNFDRSSSTFSGIKELARRFALTFG
LDQLKTREAIAMLHKDGIEFAFKEPNPQGESHPPLNLAFLDILSEFSSKLLRQDKRTVYV
YLEKFMTFQMSLRREDVWLPLMSYRNSLLAGGDDDTMSVISGISSRGSTVRSKKSKPSTG
KRKVVEGMQLSLTEESSSSDSMWLSREQTLHTPVMMQTPQLTSTIMREPKRLRPEDSFMS
VYPMQTEHHQTPLDYNRRGTSLMEDDEEPIVEDVMMSSEGRIEDLNEGMDFDTMDIDLPP
SKNRRERTELKPDFFDPASIMDESVLGVSMFSSLAEENLYFQSWSHPQFEKGGGSGGGSG
GGSWSHPQFEK
Sequence of entity 2 (B), FASTA
>9HMS_2 Double-strand-break repair protein rad21 homolog (chains B)
DITVKETKAKRKRKLIVDSVKELDSKTIRAQLSDYSDIVTTLDLAPPTKKLMMWKETGGV
EKLFSLPAQPLWNNRLLKLFTRCLTPLVPEDLRKRRKGGEADNLDEFLKEFENPEVPRED
QQQQHQQRDVIDEPIIEEPSRLQESVMEASRTNIDESAMPPPPPQGVKRKAGQIDPEPVM
PPQQVEQMEIPPVELPPEEPPNICQLIPELELLPEKEKEKEKEKEDDEEEEDEDASGGDQ
D
Sequence of entity 3 (C), FASTA
>9HMS_3 Separin (chains C)
MDYKDHDGDYKDHDIDYKDDDDKSGPGGSGGSGGGSGGGSGENLYFQGGGSGGSGMRSFK
RVNFGTLLSSQKEAEELLPDLKEFLSNPPAGFPSSRSDAERRQACDAILRACNQQLTAKL
ACPRHLGSLLELAELACDGYLVSTPQRPPLYLERILFVLLRNAAAQGSPEVTLRLAQPLH
ACLVQCSREAAPQDYEAVARGSFSLLWKGAEALLERRAAFAARLKALSFLVLLEDESTPC
EVPHFASPTACRAVAAHQLFDASGHGLNEADADFLDDLLSRHVIRALVGERGSSSGLLSP
QRALCLLELTLEHCRRFCWSRHHDKAISAVEKAHSYLRNTNLAPSLQLCQLGVKLLQVGE
EGPQAVAKLLIKASAVLSKSMEAPSPPLRALYESCQFFLSGLERGTKRRYRLDAILSLFA
FLGGYCSLLQQLRDDGVYGGSSKQQQSFLQMYFQGLHLYTVVVYDFAQGCQIVDLADLTQ
LVDSCKSTVVWMLEALEGLSGQELTDHMGMTASYTSNLAYSFYSHKLYAEACAISEPLCQ
HLGLVKPGTYPEVPPEKLHRCFRLQVESLKKLGKQAQGCKMVILWLAALQPCSPEHMAEP
VTFWVRVKMDAARAGDKELQLKTLRDSLSGWDPETLALLLREELQAYKAVRADTGQERFN
IICDLLELSPEETPAGAWARATHLVELAQVLCYHDFTQQTNCSALDAIREALQLLDSVRP
EAQARDQLLDDKAQALLWLYICTLEAKMQEGIERDRRAQAPGNLEEFEVNDLNYEDKLQE
DRFLYSNIAFNLAADAAQSKCLDQALALWKELLTKGQAPAVRCLQQTAASLQILAALYQL
VAKPMQALEVLLLLRIVSERLKDHSKAAGSSCHITQLLLTLGCPSYAQLHLEEAASSLKH
LDQTTDTYLLLSLTCDLLRSQLYWTHQKVTKGVSLLLSVLRDPALQKSSKAWYLLRVQVL
QLVAAYLSLPSNNLSHSLWEQLCAQGWQTPEIALIDSHKLLRSIILLLMGSDILSTQKAA
VETSFLDYGENLVQKWQVLSEVLSCSEKLVCHLGRLGSVSEAKAFCLEALKLTTKLQIPR
QCALFLVLKGELELARNDIDLCQSDLQQVLFLLESCTEFGGVTQHLDSVKKVHLQKGKQQ
AQVPCPPQLPEEELFLRGPALELVATVAKEPGPIAPSTNSSPVLKTKPQPIPNFLSHSPT
CDCSLCASPVLTAVCLRWVLVTAGVRLAMGHQAQGLDLLQVVLKGCPEAAERLTQALQAS
LNHKTPPSLVPSLLDEILAQAYTLLALEGLNQPSNESLQKVLQSGLKFVAARIPHLEPWR
ASLLLIWALTKLGGLSCCTTQLFASSWGWQPPLIKSVPGSEPSKTQGQKRSGRGRQKLAS
APLSLNNTSQKGLEGRGLPCTPKPPDRIRQAGPHVPFTVFEEVCPTESKPEVPQAPRVQQ
RVQTRLKVNFSDDSDLEDPVSAEAWLAEEPKRRGTASRGRGRARKGLSLKTDAVVAPGSA
PGNPGLNGRSRRAKKVASRHCEERRPQRASDQARPGGLEVLFQGPGSGDSSKKKLPSPCP
DKESDKDLGPRLQLPSAPVATGLSTLDSICDSLSVAFRGISHCPPSGLYAHLCRFLALCL
GHRDPYATAFLVTESVSITCRHQLLTHLHRQLSKAQKHRGSLEIADQLQGLSLQEMPGDV
PLARIQRLFSFRALESGHFPQPEKESFQERLALIPSGVTVCVLALATLQPGTVGNTLLLT
RLEKDSPPVSVQIPTGQNKLHLRSVLNEFDAIQKAQKENSSCTDKREWWTGRLALDHRME
VLIASLEKSVLGCWKGLLLPSSEEPGPAQEASRLQELLQDCGWKYPDRTLLKIMLSGAGA
LTPQDIQALAYGLCPTQPERAQELLNEAVGRLQGLTVPSNSHLVLVLDKDLQKLPWESMP
SLQALPVTRLPSFRFLLSYSIIKEYGASPVLSQGVDPRSTFYVLNPHNNLSSTEEQFRAN
FSSEAGWRGVVGEVPRPEQVQEALTKHDLYIYAGHGAGARFLDGQAVLRLSCRAVALLFG
SSSAALAVHGNLEGAGIVLKYIMAGCPLFLGNLWDVTDRDIDRYTEALLQGWLGAGPGAP
LLYYVNQARQAPRLKYLIGAAPIAYGLPVSLRSSLAEENLYFQSWSHPQFEKGGGSGGGS
GGGSWSHPQFEK

Ligands and cofactors

IDNameFormulaCopies
ZNZinc ionZn1

Primary citation

Substrate recognition by human separase. Yu, J., Schmidt, S., Botto, M. et al. Sci Adv (2025) 11:eady9807-eady9807. DOI 10.1126/sciadv.ady9807 · PubMed

Other PDB entries of the same protein (UniProt Q8N3U4 (AlphaFold model), which also has an AlphaFold model), best resolution first:

Browse structure collections

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