9HN5: Human separase

Cryo-EM structure of human separase bound to phosphorylated SCC1 (100-320 aa). Determined by electron microscopy at 2.96 Å resolution. Released 3 Sept 2025.

Method
Electron microscopy
Resolution
2.96 Å
Organism
Homo sapiens
Chains
2
Atoms
11,314
Mol. weight
263.67 kDa
Ligands
ZN
Released
3 Sept 2025

Explore 9HN5 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9HN5 contains 85 α-helices and 17 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: 82 helices, 16 β-strands

ElementResiduesLengthSheet
α-helix247-26216
α-helix268-28114
α-helix287-30317
α-helix308-32720
α-helix333-35018
α-helix357-37923
α-helix381-3855
α-helix387-41327
α-helix421-44121
α-helix447-46923
α-helix473-48917
α-helix500-51617
α-helix521-53313
α-helix539-55820
α-helix563-5664
α-helix578-59417
α-helix600-61314
α-helix619-63820
α-helix642-6454
α-helix649-66113
α-helix670-70233
α-helix729-7335
α-helix737-75923
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-helix916-9183
α-helix921-9288
α-helix935-95319
α-helix956-9583
α-helix975-100127
α-helix1004-102118
α-helix1024-104017
α-helix1044-106118
α-helix1139-11413
α-helix1149-11524
α-helix1154-117320
α-helix1177-120630
α-helix1211-12122
α-helix1220-123617
α-helix1243-125614
α-helix1262-127716
α-helix1287-12915
α-helix1573-158816
α-helix1594-160815
α-helix1609-16113
α-helix1613-162210
α-helix1626-164520
α-helix1668-167710
α-helix1689-169911
α-helix1702-17032
β-strand1706-171492
α-helix17151
β-strand1724-173072
β-strand1737-174262
α-helix1750-176718
α-helix1773-179422
α-helix1795-17995
α-helix1800-18067
α-helix1808-18103
α-helix1814-182916
α-helix1836-18449
α-helix1846-18483
α-helix1851-186111
α-helix1866-187914
α-helix1884-18863
β-strand1890-189452
α-helix1904-19063
α-helix1908-19103
β-strand1915-191732
α-helix1921-193212
α-helix1937-19404
β-strand194313
β-strand1948-195252
α-helix1959-197012
β-strand1975-197952
α-helix1982-19843
α-helix1985-199410
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-helix2066-208318
α-helix2089-20957
α-helix2096-20983
β-strand2110-211452
β-strand211913
Chain B: 3 helices, 1 β-strand
ElementResiduesLengthSheet
α-helix168-1703
β-strand17111
α-helix172-1732
α-helix191-1955

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
Double-strand-break repair protein rad21 homologBprotein227Homo sapiensO60216 (AlphaFold model)
SeparinAprotein2172Homo sapiensQ14674 (AlphaFold model)
Sequence of entity 1 (B), FASTA
>9HN5_1 Double-strand-break repair protein rad21 homolog (chains B)
NREAAYNAITLPEEFHDFDQPLPDLDDIDVAQQFSLIQSRVEEITMREEVGNISILQEND
FGDFGMDDREIMREGSAFEDDDMLVSTTTSNLLLESEQSTSNLNEKINHLEYEDQYKDDN
FGEGNDGGILDDKLISNNDGGIFDDEIMREGPPALSEAGVMLPEQPAHDDMDEDDNVSMG
GPDSPDSVDPVEPMPTMTDQTTLVPNEEEAFALEPIDITVKETKAKR
Sequence of entity 2 (A), FASTA
>9HN5_2 Separin (chains A)
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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