9HMA: Apo human separase

Cryo-EM structure of apo human separase. Determined by electron microscopy at 3.3 Å resolution. Released 3 Sept 2025.

Method
Electron microscopy
Resolution
3.3 Å
Organism
Homo sapiens
Chains
1
Atoms
10,333
Mol. weight
243.22 kDa
Ligands
ZN
Released
3 Sept 2025

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

Secondary structure: helices and β-sheets

9HMA contains 75 α-helices and 15 β-strands across 1 chain. 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: 75 helices, 15 β-strands

ElementResiduesLengthSheet
α-helix330-34920
α-helix358-38023
α-helix391-41323
α-helix419-44123
α-helix448-4503
α-helix452-46918
α-helix530-54617
α-helix557-57418
α-helix578-59013
α-helix596-5994
α-helix600-61516
α-helix620-6234
α-helix626-6305
α-helix635-65117
α-helix657-67014
α-helix676-69318
α-helix706-71914
α-helix724-7263
α-helix727-76034
α-helix776-7816
α-helix786-7905
α-helix796-81621
α-helix820-8212
α-helix826-84217
α-helix846-86217
α-helix866-88318
α-helix887-90014
α-helix908-92720
α-helix931-94313
α-helix945-9484
α-helix952-96817
α-helix978-9858
α-helix992-101120
α-helix1032-105827
α-helix1062-107817
α-helix1081-109717
α-helix1101-111818
α-helix1195-11984
α-helix1206-12094
α-helix1211-123020
α-helix1237-126327
α-helix1275-129319
α-helix1298-13003
α-helix1303-131311
α-helix1315-13173
α-helix1319-133416
α-helix1343-13453
α-helix1630-164516
α-helix1653-166513
α-helix1666-16683
α-helix1670-16789
α-helix1683-170018
α-helix1725-173410
α-helix1746-175611
α-helix1759-17602
β-strand1763-177191
β-strand1781-178881
β-strand1791-179991
α-helix1807-182519
α-helix1830-185021
α-helix1851-18566
α-helix1857-18637
α-helix1872-188615
α-helix1893-19008
α-helix1908-191811
α-helix1923-193715
β-strand1947-195261
α-helix1961-19633
β-strand1972-197431
α-helix1978-198912
α-helix1995-19984
β-strand2005-200951
α-helix2017-202711
β-strand2032-203651
α-helix2039-20413
α-helix2042-20509
β-strand2054-205741
α-helix2069-20735
β-strand2080-208341
β-strand209212
α-helix2098-20992
β-strand210012
α-helix2102-21087
β-strand2113-211751
α-helix2126-213813
β-strand214513
α-helix2146-21527
α-helix2153-21553
β-strand2167-217151
β-strand217513

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
SeparinAprotein2217Homo sapiensQ14674 (AlphaFold model)
Sequence of entity 1 (A), FASTA
>9HMA_1 Separin (chains A)
MSGDYKDHDGDYKDHDIDYKDDDDKSGPGGSGGSGGGSGGGSGENLYFQGGGSGGSGMRS
FKRVNFGTLLSSQKEAEELLPDLKEFLSNPPAGFPSSRSDAERRQACDAILRACNQQLTA
KLACPRHLGSLLELAELACDGYLVSTPQRPPLYLERILFVLLRNAAAQGSPEVTLRLAQP
LHACLVQCSREAAPQDYEAVARGSFSLLWKGAEALLERRAAFAARLKALSFLVLLEDEST
PCEVPHFASPTACRAVAAHQLFDASGHGLNEADADFLDDLLSRHVIRALVGERGSSSGLL
SPQRALCLLELTLEHCRRFCWSRHHDKAISAVEKAHSYLRNTNLAPSLQLCQLGVKLLQV
GEEGPQAVAKLLIKASAVLSKSMEAPSPPLRALYESCQFFLSGLERGTKRRYRLDAILSL
FAFLGGYCSLLQQLRDDGVYGGSSKQQQSFLQMYFQGLHLYTVVVYDFAQGCQIVDLADL
TQLVDSCKSTVVWMLEALEGLSGQELTDHMGMTASYTSNLAYSFYSHKLYAEACAISEPL
CQHLGLVKPGTYPEVPPEKLHRCFRLQVESLKKLGKQAQGCKMVILWLAALQPCSPEHMA
EPVTFWVRVKMDAARAGDKELQLKTLRDSLSGWDPETLALLLREELQAYKAVRADTGQER
FNIICDLLELSPEETPAGAWARATHLVELAQVLCYHDFTQQTNCSALDAIREALQLLDSV
RPEAQARDQLLDDKAQALLWLYICTLEAKMQEGIERDRRAQAPGNLEEFEVNDLNYEDKL
QEDRFLYSNIAFNLAADAAQSKCLDQALALWKELLTKGQAPAVRCLQQTAASLQILAALY
QLVAKPMQALEVLLLLRIVSERLKDHSKAAGSSCHITQLLLTLGCPSYAQLHLEEAASSL
KHLDQTTDTYLLLSLTCDLLRSQLYWTHQKVTKGVSLLLSVLRDPALQKSSKAWYLLRVQ
VLQLVAAYLSLPSNNLSHSLWEQLCAQGWQTPEIALIDSHKLLRSIILLLMGSDILSTQK
AAVETSFLDYGENLVQKWQVLSEVLSCSEKLVCHLGRLGSVSEAKAFCLEALKLTTKLQI
PRQCALFLVLKGELELARNDIDLCQSDLQQVLFLLESCTEFGGVTQHLDSVKKVHLQKGK
QQAQVPCPPQLPEEELFLRGPALELVATVAKEPGPIAPSTNSSPVLKTKPQPIPNFLSHS
PTCDCSLCASPVLTAVCLRWVLVTAGVRLAMGHQAQGLDLLQVVLKGCPEAAERLTQALQ
ASLNHKTPPSLVPSLLDEILAQAYTLLALEGLNQPSNESLQKVLQSGLKFVAARIPHLEP
WRASLLLIWALTKLGGLSCCTTQLFASSWGWQPPLIKSVPGSEPSKTQGQKRSGRGRQKL
ASAPLSLNNTSQKGLEGRGLPCTPKPPDRIRQAGPHVPFTVFEEVCPTESKPEVPQAPRV
QQRVQTRLKVNFSDDSDLEDPVSAEAWLAEEPKRRGTASRGRGRARKGLSLKTDAVVAPG
SAPGNPGLNGRSRRAKKVASRHCEERRPQRASDQARPGPEIMRTIPEEELTDNWRKMSFE
ILRGSDGEDSASGGKTPAPGPEAASGEWELLRLDSSKKKLPSPCPDKESDKDLGPRLQLP
SAPVATGLSTLDSICDSLSVAFRGISHCPPSGLYAHLCRFLALCLGHRDPYATAFLVTES
VSITCRHQLLTHLHRQLSKAQKHRGSLEIADQLQGLSLQEMPGDVPLARIQRLFSFRALE
SGHFPQPEKESFQERLALIPSGVTVCVLALATLQPGTVGNTLLLTRLEKDSPPVSVQIPT
GQNKLHLRSVLNEFDAIQKAQKENSSCTDKREWWTGRLALDHRMEVLIASLEKSVLGCWK
GLLLPSSEEPGPAQEASRLQELLQDCGWKYPDRTLLKIMLSGAGALTPQDIQALAYGLCP
TQPERAQELLNEAVGRLQGLTVPSNSHLVLVLDKDLQKLPWESMPSLQALPVTRLPSFRF
LLSYSIIKEYGASPVLSQGVDPRSTFYVLNPHNNLSSTEEQFRANFSSEAGWRGVVGEVP
RPEQVQEALTKHDLYIYAGHGAGARFLDGQAVLRLSCRAVALLFGCSSAALAVHGNLEGA
GIVLKYIMAGCPLFLGNLWDVTDRDIDRYTEALLQGWLGAGPGAPLLYYVNQARQAPRLK
YLIGAAPIAYGLPVSLRSSLAEENLYFQSWSHPQFEKGGGSGGGSGGGSWSHPQFEK

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 Q14674 (AlphaFold model), which also has an AlphaFold model), best resolution first:

Browse structure collections

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