9HN0: Human separase

Cryo-EM structure of human separase bound to SCC1 (310-550 aa). Determined by electron microscopy at 2.8 Å resolution. Released 3 Sept 2025.

Method: Electron microscopy
Resolution: 2.8 Å
Organism: Homo sapiens
Chains: 2
Atoms: 12,466
Mol. weight: 265.84 kDa
Ligands: ZN
Released: 3 Sept 2025

Explore 9HN0 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9HN0 contains 95 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: 1 helix, 1 β-strand

Element	Residues	Length	Sheet
α-helix	423-425	3
β-strand	426	1	1

Chain B: 94 helices, 18 β-strands

Element	Residues	Length	Sheet
α-helix	47-62	16
α-helix	68-88	21
α-helix	96-111	16
α-helix	114-120	7
α-helix	124-131	8
α-helix	138-143	6
α-helix	145-157	13
α-helix	162-175	14
α-helix	182-185	4
α-helix	193-204	12
α-helix	214-223	10
α-helix	224-229	6
α-helix	230-233	4
α-helix	242-244	3
α-helix	245-264	20
α-helix	269-280	12
α-helix	288-303	16
α-helix	308-327	20
α-helix	333-349	17
α-helix	357-379	23
α-helix	382-385	4
α-helix	387-413	27
α-helix	420-425	6
α-helix	427-441	15
α-helix	447-469	23
α-helix	473-489	17
α-helix	491	1
α-helix	500-517	18
α-helix	520-533	14
α-helix	543-558	16
α-helix	563-566	4
α-helix	569-572	4
β-strand	574	1	2
β-strand	576	1	2
α-helix	578-594	17
α-helix	600-613	14
α-helix	619-637	19
α-helix	642-645	4
α-helix	649-661	13
α-helix	670-703	34
α-helix	732-735	4
α-helix	738-759	22
α-helix	763-764	2
α-helix	769-785	17
α-helix	789-806	18
α-helix	809-826	18
α-helix	829-842	14
α-helix	843-845	3
α-helix	851-870	20
α-helix	874-885	12
α-helix	888-891	4
α-helix	895-912	18
α-helix	916-918	3
α-helix	921-928	8
α-helix	935-954	20
α-helix	975-1001	27
α-helix	1004-1021	18
α-helix	1024-1040	17
α-helix	1044-1061	18
α-helix	1149-1152	4
α-helix	1154-1173	20
α-helix	1180-1206	27
α-helix	1211-1212	2
α-helix	1220-1236	17
α-helix	1241-1255	15
α-helix	1262-1277	16
α-helix	1287-1291	5
α-helix	1573-1588	16
α-helix	1594-1608	15
α-helix	1609-1611	3
α-helix	1613-1621	9
α-helix	1626-1646	21
α-helix	1668-1677	10
α-helix	1689-1700	12
α-helix	1702-1703	2
β-strand	1706-1714	9	3
β-strand	1724-1730	7	3
β-strand	1737-1742	6	3
α-helix	1750-1769	20
α-helix	1773-1793	21
α-helix	1794-1799	6
α-helix	1800-1805	6
α-helix	1808-1810	3
α-helix	1814-1827	14
α-helix	1836-1844	9
α-helix	1851-1861	11
α-helix	1866-1880	15
β-strand	1890-1895	6	3
α-helix	1899-1901	3
α-helix	1904-1906	3
α-helix	1908-1910	3
β-strand	1915-1917	3	3
α-helix	1921-1932	12
β-strand	1943	1	4
β-strand	1948-1952	5	3
α-helix	1959-1971	13
β-strand	1976-1979	4	3
α-helix	1985-1994	10
β-strand	1997-2001	5	3
α-helix	2012-2016	5
β-strand	2023-2026	4	3
β-strand	2035	1	5
α-helix	2041-2042	2
β-strand	2043	1	5
α-helix	2045-2052	8
β-strand	2056-2060	5	3
β-strand	2065	1	1
α-helix	2066-2083	18
α-helix	2089-2096	8
α-helix	2103-2107	5
β-strand	2110-2114	5	3
β-strand	2119	1	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Double-strand-break repair protein rad21 homolog	A	protein	241	Homo sapiens	O60216 (AlphaFold model)
Separin	B	protein	2172	Homo sapiens	Q14674 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>9HN0_1 Double-strand-break repair protein rad21 homolog (chains A)
DITVKETKAKRKRKLIVDSVKELDSKTIRAQLSDYSDIVTTLDLAPPTKKLMMWKETGGV
EKLFSLPAQPLWNNRLLKLFTRCLTPLVPEDLRKRRKGGEADNLDEFLKEFENPEVPRED
QQQQHQQRDVIDEPIIEEPSRLQESVMEASRTNIDESAMPPPPPQGVKRKAGQIDPEPVM
PPQQVEQMEIPPVELPPEEPPNICQLIPELELLPEKEKEKEKEKEDDEEEEDEDASGGDQ
D

Sequence of entity 2 (B), FASTA

>9HN0_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

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	1

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:

8ROE 1.36 Å, Human cohesin SMC1A-HD(shortCC-EQ)/RAD21-C complex - ADP-bound conformation
8ROD 1.5 Å, Human cohesin SMC1A-HD(shortCC-EQ)/RAD21-C complex - Open/closed P-loop conformation
8ROF 1.65 Å, Human cohesin SMC1A-HD(shortCC-EQ)/RAD21-C complex - ADP-Mg-bound conformation
8RO9 1.77 Å, Human cohesin SMC1A-HD(longCC-EQ)/RAD21-C complex - Open/closed P-loop conformation
8ROC 1.85 Å, Human cohesin SMC1A-HD(shortCC-EQ)/RAD21-C complex - Apo closed P-loop conformation
8RO8 1.9 Å, Human cohesin SMC1A-HD(longCC-EQ)/RAD21-C complex - Apo closed P-loop conformation
8ROG 1.94 Å, Human cohesin SMC1A-HD(shortCC-EQ)/RAD21-C complex - ATPgS-Mg-bound conformation
8RO7 2.09 Å, Human cohesin SMC1A-HD(longCC)/RAD21-C complex - Open/closed P-loop conformation
8RO6 2.2 Å, Human cohesin SMC1A-HD(longCC)/RAD21-C complex - Apo closed P-loop conformation
8ROK 2.25 Å, Human cohesin SMC3-HD(EQ)/RAD21-N complex - ATP-Mg-bound conformation - Form 1
6RRC 2.37 Å, Crystal structure of the N-terminal region of human cohesin subunit STAG1 in complex…
8ROA 2.44 Å, Human cohesin SMC1A-HD(longCC-EQ)/RAD21-C complex - ADP-bound conformation

Browse structure collections

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