9HVY: Human separase-SCC1 (1-631) fusion protein

Cryo-EM structure of human separase-SCC1 (1-631) fusion protein. Determined by electron microscopy at 3.5 Å resolution. Released 14 Jan 2026.

Method: Electron microscopy
Resolution: 3.5 Å
Organism: Homo sapiens
Chains: 1
Atoms: 10,456
Mol. weight: 311.24 kDa
Ligands: ZN
Released: 14 Jan 2026

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

Secondary structure: helices and β-sheets

9HVY contains 78 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: 78 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	332-351	20
α-helix	354-356	3
α-helix	357-379	23
α-helix	389-414	26
α-helix	420-441	22
α-helix	448-452	5
α-helix	453-469	17
α-helix	474-488	15
α-helix	500-517	18
α-helix	520-533	14
α-helix	539-559	21
α-helix	562-566	5
α-helix	569-573	5
α-helix	578-594	17
α-helix	600-613	14
α-helix	619-638	20
α-helix	642-644	3
α-helix	649-662	14
α-helix	670-702	33
α-helix	719-724	6
α-helix	729-733	5
α-helix	739-759	21
α-helix	763-764	2
α-helix	769-785	17
α-helix	789-806	18
α-helix	809-826	18
α-helix	829-843	15
α-helix	851-870	20
α-helix	874-885	12
α-helix	895-911	17
α-helix	921-928	8
α-helix	935-953	19
α-helix	956-958	3
α-helix	976-1001	26
α-helix	1004-1021	18
α-helix	1024-1040	17
α-helix	1044-1061	18
α-helix	1139-1141	3
α-helix	1149-1152	4
α-helix	1154-1174	21
α-helix	1180-1206	27
α-helix	1211-1212	2
α-helix	1220-1236	17
α-helix	1242-1256	15
α-helix	1262-1277	16
α-helix	1289-1291	3
α-helix	1573-1585	13
α-helix	1594-1608	15
α-helix	1609-1611	3
α-helix	1613-1621	9
α-helix	1626-1643	18
α-helix	1668-1677	10
α-helix	1689-1700	12
α-helix	1702-1703	2
β-strand	1706-1713	8	1
β-strand	1724-1730	7	1
β-strand	1737-1742	6	1
α-helix	1750-1768	19
α-helix	1773-1793	21
α-helix	1794-1799	6
α-helix	1800-1802	3
α-helix	1803-1806	4
α-helix	1808-1809	2
α-helix	1814-1827	14
α-helix	1836-1844	9
α-helix	1851-1861	11
α-helix	1866-1880	15
α-helix	1883-1886	4
β-strand	1890-1895	6	1
α-helix	1904-1906	3
α-helix	1908-1910	3
β-strand	1915-1917	3	1
α-helix	1922-1932	11
α-helix	1937-1940	4
β-strand	1943	1	2
β-strand	1948-1952	5	1
α-helix	1960-1964	5
α-helix	1967-1970	4
β-strand	1975-1979	5	1
α-helix	1982-1984	3
α-helix	1985-1993	9
β-strand	1997-2000	4	1
α-helix	2012-2017	6
β-strand	2023-2026	4	1
β-strand	2035	1	3
α-helix	2041-2042	2
β-strand	2043	1	3
α-helix	2045-2051	7
β-strand	2056-2060	5	1
α-helix	2068-2083	16
α-helix	2089-2096	8
β-strand	2110-2114	5	1
β-strand	2119	1	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Double-strand-break repair protein rad21 homolog,Separin	A	protein	2819	Homo sapiens	O60216 (AlphaFold model), Q14674 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>9HVY_1 Double-strand-break repair protein rad21 homolog,Separin (chains A)
MFYAHFVLSKRGPLAKIWLAAHWDKKLTKAHVFECNLESSVESIISPKVKMALRTSGHLL
LGVVRIYHRKAKYLLADCNEAFIKIKMAFRPGVVDLPEENREAAYNAITLPEEFHDFDQP
LPDLDDIDVAQQFSLNQSRVEEITMREEVGNISILQENDFGDFGMDDREIMREGSAFEDD
DMLVSTTTSNLLLESEQSTSNLNEKINHLEYEDQYKDDNFGEGNDGGILDDKLISNNDGG
IFDDPPALSEAGVMLPEQPAHDDMDEDDNVSMGGPDSPDSVDPVEPMPTMTDQTTLVPNE
EEAFALEPIDITVKETKAKRKRKLIVDSVKELDSKTIRAQLSDYSDIVTTLDLAPPTKKL
MMWKETGGVEKLFSLPAQPLWNNRLLKLFTRCLTPLVPEDLRKRRKGGEADNLDEFLKEF
ENPEVPREDQQQQHQQRDVIDEPIIEEPSRLQESVMEASRTNIDESAMPPPPPQGVKRKA
GQIDPEPVMPPQQVEQMEIPPVELPPEEPPNICQLIPELELLPEKEKEKEKEKEDDEEEE
DEDASGGDQDQEERRWNKRTQQMLHGLQRALAKTGAESISLLELCRNTNRKQAAAKFYSF
LVLKKQQAIELTQEEPYSDIIATPGPRFHIIGGSGGGGSGGGGSGGSGGSGGGSGGGSGM
RSFKRVNFGTLLSSQKEAEELLPDLKEFLSNPPAGFPSSRSDAERRQACDAILRACNQQL
TAKLACPRHLGSLLELAELACDGYLVSTPQRPPLYLERILFVLLRNAAAQGSPEVTLRLA
QPLHACLVQCSREAAPQDYEAVARGSFSLLWKGAEALLERRAAFAARLKALSFLVLLEDE
STPCEVPHFASPTACRAVAAHQLFDASGHGLNEADADFLDDLLSRHVIRALVGERGSSSG
LLSPQRALCLLELTLEHCRRFCWSRHHDKAISAVEKAHSYLRNTNLAPSLQLCQLGVKLL
QVGEEGPQAVAKLLIKASAVLSKSMEAPSPPLRALYESCQFFLSGLERGTKRRYRLDAIL
SLFAFLGGYCSLLQQLRDDGVYGGSSKQQQSFLQMYFQGLHLYTVVVYDFAQGCQIVDLA
DLTQLVDSCKSTVVWMLEALEGLSGQELTDHMGMTASYTSNLAYSFYSHKLYAEACAISE
PLCQHLGLVKPGTYPEVPPEKLHRCFRLQVESLKKLGKQAQGCKMVILWLAALQPCSPEH
MAEPVTFWVRVKMDAARAGDKELQLKTLRDSLSGWDPETLALLLREELQAYKAVRADTGQ
ERFNIICDLLELSPEETPAGAWARATHLVELAQVLCYHDFTQQTNCSALDAIREALQLLD
SVRPEAQARDQLLDDKAQALLWLYICTLEAKMQEGIERDRRAQAPGNLEEFEVNDLNYED
KLQEDRFLYSNIAFNLAADAAQSKCLDQALALWKELLTKGQAPAVRCLQQTAASLQILAA
LYQLVAKPMQALEVLLLLRIVSERLKDHSKAAGSSCHITQLLLTLGCPSYAQLHLEEAAS
SLKHLDQTTDTYLLLSLTCDLLRSQLYWTHQKVTKGVSLLLSVLRDPALQKSSKAWYLLR
VQVLQLVAAYLSLPSNNLSHSLWEQLCAQGWQTPEIALIDSHKLLRSIILLLMGSDILST
QKAAVETSFLDYGENLVQKWQVLSEVLSCSEKLVCHLGRLGSVSEAKAFCLEALKLTTKL
QIPRQCALFLVLKGELELARNDIDLCQSDLQQVLFLLESCTEFGGVTQHLDSVKKVHLQK
GKQQAQVPCPPQLPEEELFLRGPALELVATVAKEPGPIAPSTNSSPVLKTKPQPIPNFLS
HSPTCDCSLCASPVLTAVCLRWVLVTAGVRLAMGHQAQGLDLLQVVLKGCPEAAERLTQA
LQASLNHKTPPSLVPSLLDEILAQAYTLLALEGLNQPSNESLQKVLQSGLKFVAARIPHL
EPWRASLLLIWALTKLGGLSCCTTQLFASSWGWQPPLIKSVPGSEPSKTQGQKRSGRGRQ
KLASAPLSLNNTSQKGLEGRGLPCTPKPPDRIRQAGPHVPFTVFEEVCPTESKPEVPQAP
RVQQRVQTRLKVNFSDDSDLEDPVSAEAWLAEEPKRRGTASRGRGRARKGLSLKTDAVVA
PGSAPGNPGLNGRSRRAKKVASRHCEERRPQRASDQARPGPEIMRTIPEEELTDNWRKMS
FEILRGSDGEDSASGGKTPAPGPEAASGEWELLRLDSSKKKLPSPCPDKESDKDLGPRLQ
LPSAPVATGLSTLDSICDSLSVAFRGISHCPPSGLYAHLCRFLALCLGHRDPYATAFLVT
ESVSITCRHQLLTHLHRQLSKAQKHRGSLEIADQLQGLSLQEMPGDVPLARIQRLFSFRA
LESGHFPQPEKESFQERLALIPSGVTVCVLALATLQPGTVGNTLLLTRLEKDSPPVSVQI
PTGQNKLHLRSVLNEFDAIQKAQKENSSCTDKREWWTGRLALDHRMEVLIASLEKSVLGC
WKGLLLPSSEEPGPAQEASRLQELLQDCGWKYPDRTLLKIMLSGAGALTPQDIQALAYGL
CPTQPERAQELLNEAVGRLQGLTVPSNSHLVLVLDKDLQKLPWESMPSLQALPVTRLPSF
RFLLSYSIIKEYGASPVLSQGVDPRSTFYVLNPHNNLSSTEEQFRANFSSEAGWRGVVGE
VPRPEQVQEALTKHDLYIYAGHGAGARFLDGQAVLRLSCRAVALLFGSSSAALAVHGNLE
GAGIVLKYIMAGCPLFLGNLWDVTDRDIDRYTEALLQGWLGAGPGAPLLYYVNQARQAPR
LKYLIGAAPIAYGLPVSLRSSLAEENLYFQSWSHPQFEKGGGSGGGSGGGSWSHPQFEK

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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