9HM7: Apo human separase with the mutation C2029S

Cryo-EM structure of apo human separase with the mutation C2029S. Determined by electron microscopy at 3.1 Å resolution. Released 3 Sept 2025.

Method
Electron microscopy
Resolution
3.1 Å
Organism
Homo sapiens
Chains
1
Atoms
10,150
Mol. weight
243.2 kDa
Ligands
ZN
Released
3 Sept 2025

Explore 9HM7 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9HM7 contains 70 α-helices and 17 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: 70 helices, 17 β-strands

ElementResiduesLengthSheet
α-helix423-44119
α-helix447-46923
α-helix473-49018
α-helix502-51615
α-helix521-53313
α-helix544-55916
α-helix562-5665
α-helix569-5735
α-helix578-59417
α-helix600-61314
α-helix619-63820
α-helix642-6454
α-helix649-66113
α-helix670-6734
α-helix677-70327
α-helix711-7144
α-helix719-7235
α-helix739-75921
α-helix763-7642
α-helix769-78517
α-helix789-80618
α-helix809-82517
α-helix829-84315
α-helix851-87020
α-helix874-88512
α-helix888-8914
α-helix895-91218
α-helix916-9183
α-helix921-9288
α-helix935-95319
α-helix975-100127
α-helix1004-102118
α-helix1024-104017
α-helix1044-106118
α-helix1154-117320
α-helix1180-120627
α-helix1215-12162
α-helix1220-123617
α-helix1242-125514
α-helix1262-127716
α-helix1286-12916
α-helix1481-14844
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-strand1706-171491
β-strand1724-173071
β-strand1737-174261
α-helix1750-176718
α-helix1773-179321
α-helix1794-17996
α-helix1800-18067
α-helix1814-182916
α-helix1836-18449
α-helix1846-18483
α-helix1851-186111
α-helix1866-188015
β-strand1890-189561
α-helix1904-19063
β-strand1915-191731
α-helix1921-193212
α-helix1937-19404
β-strand194312
β-strand1948-195251
α-helix1959-197113
β-strand1975-197951
α-helix1982-19843
α-helix1985-199410
β-strand1997-200151
α-helix2012-20165
β-strand2023-202751
β-strand203513
α-helix2041-20422
β-strand204313
α-helix2045-20517
β-strand2056-206051
α-helix2066-208116
β-strand208814
α-helix2089-20968
β-strand2110-211451
β-strand211814
β-strand211912

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
SeparinAprotein2217Homo sapiensQ14674 (AlphaFold model)
Sequence of entity 1 (A), FASTA
>9HM7_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
RPEQVQEALTKHDLYIYAGHGAGARFLDGQAVLRLSCRAVALLFGSSSAALAVHGNLEGA
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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