9HN4: Human separase

Cryo-EM structure of human separase bound to phosphorylated SCC1 (310-550 aa). Determined by electron microscopy at 2.93 Å resolution. Released 3 Sept 2025.

Method
Electron microscopy
Resolution
2.93 Å
Organism
Homo sapiens
Chains
2
Atoms
10,855
Mol. weight
265.92 kDa
Ligands
ZN
Released
3 Sept 2025

Explore 9HN4 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9HN4 contains 79 α-helices and 19 β-strands across 2 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: 4 helices, 1 β-strand

ElementResiduesLengthSheet
α-helix422-4254
β-strand42611
α-helix444-4496
α-helix451-4555
α-helix468-4703
Chain B: 75 helices, 18 β-strands
ElementResiduesLengthSheet
α-helix308-32720
α-helix333-35018
α-helix358-37922
α-helix381-3855
α-helix387-41428
α-helix420-44122
α-helix447-46923
α-helix473-48917
α-helix4911
α-helix500-51617
α-helix520-53314
α-helix539-55921
α-helix563-5664
α-helix569-5735
α-helix578-59417
α-helix600-61314
α-helix619-63618
α-helix642-6454
α-helix649-66214
α-helix670-70334
α-helix731-7333
α-helix738-75922
α-helix763-7642
α-helix769-78517
α-helix789-80618
α-helix809-82618
α-helix829-84315
α-helix851-87020
α-helix874-88613
α-helix888-8914
α-helix895-91218
α-helix921-9288
α-helix935-95420
α-helix975-100127
α-helix1004-102118
α-helix1024-104017
α-helix1044-106320
α-helix1149-11524
α-helix1154-117320
α-helix1180-120627
α-helix1211-12122
α-helix1220-123617
α-helix1241-125515
α-helix1262-127716
α-helix1289-12913
α-helix1573-158816
α-helix1594-160815
α-helix1609-16113
α-helix1613-16219
α-helix1626-164621
α-helix1668-167710
α-helix1689-170012
α-helix1702-17032
β-strand1706-171492
β-strand1724-173182
β-strand1734-174292
α-helix1750-176819
α-helix1773-179321
α-helix1794-17996
α-helix1804-18063
α-helix1808-18103
α-helix1814-182714
α-helix1836-18438
α-helix1846-18483
α-helix1851-186111
α-helix1866-188015
β-strand1890-189562
α-helix1904-19063
β-strand1915-191732
α-helix1921-193212
α-helix1937-19404
β-strand194313
β-strand1948-195252
α-helix1960-197112
β-strand1975-197952
α-helix1982-19843
α-helix1985-19939
β-strand1997-200152
α-helix2012-20165
β-strand2023-202642
β-strand203514
α-helix2041-20422
β-strand204314
α-helix2045-20517
β-strand2056-206052
β-strand206511
α-helix2067-208115
β-strand208815
α-helix2089-20968
α-helix2103-21075
β-strand2110-211452
β-strand211815
β-strand211913

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
Double-strand-break repair protein rad21 homologAprotein241Homo sapiensO60216 (AlphaFold model)
SeparinBprotein2172Homo sapiensQ14674 (AlphaFold model)
Sequence of entity 1 (A), FASTA
>9HN4_1 Double-strand-break repair protein rad21 homolog (chains A)
DITVKETKAKRKRKLIVDSVKELDSKTIRAQLSDYSDIVTTLDLAPPTKKLMMWKETGGV
EKLFSLPAQPLWNNRLLKLFTRCLTPLVPEDLRKRRKGGEADNLDEFLKEFENPEVPRED
QQQQHQQRDVIDEPIIEEPSRLQESVMEASRTNIDESAMPPPPPQGVKRKAGQIDPEPVM
PPQQVEQMEIPPVELPPEEPPNICQLIPELELLPEKEKEKEKEKEDDEEEEDEDASGGDQ
D
Sequence of entity 2 (B), FASTA
>9HN4_2 Separin (chains B)
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 O60216 (AlphaFold model), which also has an AlphaFold model), best resolution first:

Browse structure collections

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