9EP3: SA2/SCC1/WAPL complex

Structure of the SA2/SCC1/WAPL complex. Determined by X-ray diffraction at 3.08 Å resolution. Released 1 Oct 2025.

Method: X-ray diffraction
Resolution: 3.08 Å
Organism: Homo sapiens
Chains: 3
Atoms: 8,382
Mol. weight: 132.3 kDa
Released: 1 Oct 2025

Explore 9EP3 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9EP3 contains 62 α-helices and 10 β-strands across 3 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: 57 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	83-90	8
α-helix	95-108	14
α-helix	110-124	15
α-helix	133-138	6
α-helix	141-150	10
α-helix	160-162	3
α-helix	166-186	21
α-helix	190-192	3
α-helix	196-208	13
β-strand	212	1	1
α-helix	213-254	42
α-helix	261-288	28
α-helix	289-293	5
α-helix	294-296	3
β-strand	299	1	2
α-helix	302-318	17
α-helix	320-323	4
α-helix	326-335	10
α-helix	341-355	15
α-helix	362-378	17
β-strand	381	1	3
α-helix	384-400	17
α-helix	407-414	8
α-helix	415-418	4
β-strand	419	1	4
α-helix	422-436	15
α-helix	458-470	13
α-helix	478-484	7
α-helix	489-492	4
α-helix	495-503	9
α-helix	515-533	19
α-helix	537-538	2
α-helix	547-549	3
α-helix	550-577	28
α-helix	582-588	7
α-helix	592-594	3
α-helix	599-602	4
α-helix	606-622	17
α-helix	626-639	14
α-helix	647-672	26
α-helix	681-700	20
α-helix	704-706	3
α-helix	709-722	14
α-helix	727-747	21
α-helix	755-776	22
α-helix	781-797	17
α-helix	800-803	4
α-helix	808-813	6
α-helix	819-832	14
α-helix	851-873	23
α-helix	881-886	6
α-helix	893-933	41
α-helix	943-956	14
α-helix	966-981	16
α-helix	985-986	2
α-helix	995-998	4
α-helix	999-1003	5
α-helix	1004-1009	6
α-helix	1012-1023	12
α-helix	1028-1032	5
α-helix	1039-1047	9

Chain B: 5 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	326	1	1
β-strand	331	1	2
α-helix	334-342	9
α-helix	345-347	3
β-strand	348	1	3
β-strand	351-352	2	5
β-strand	353	1	4
α-helix	358-366	9
α-helix	369-373	5
α-helix	383-390	8

Chain C: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	22-23	2	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Cohesin subunit SA-2	A	protein	981	Homo sapiens	Q8N3U4 (AlphaFold model)
Double-strand-break repair protein rad21 homolog	B	protein	140	Homo sapiens	O60216 (AlphaFold model)
Wings apart-like protein homolog	C	protein	22	Homo sapiens	Q7Z5K2 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>9EP3_1 Cohesin subunit SA-2 (chains A)
ENMMLFEVVKMGKSAMQSVVDDWIESYKHDRDIALLDLINFFIQCSGCKGVVTAEMFRHM
QNSEIIRKMTEEFDEDSGDYPLTMAGPQWKKFKSSFCEFIGVLVRQCQYSIIYDEYMMDT
VISLLTGLSDSQVRAFRHTSTLAAMKLMTALVNVALNLSINMDNTQRQYEAERNKMIGKR
ANERLELLLQKRKELQENQDEIENMMNAIFKGVFVHRYRDAIAEIRAICIEEIGIWMKMY
SDAFLNDSYLKYVGWTMHDKQGEVRLKCLTALQGLYYNKELNSKLELFTSRFKDRIVSMT
LDKEYDVAVQAIKLLTLVLQSSEEVLTAEDCENVYHLVYSAHRPVAVAAGEFLYKKLFSR
RDPEEDGMMKRRGRQGPNANLVKTLVFFFLESELHEHAAYLVDSMWDCATELLKDWECMN
SLLLEEPLSGEEALTDRQESALIEIMLCTIRQAAECHPPVGRGTGKRVLTAKEKKTQLDD
RTKITELFAVALPQLLAKYSVDAEKVTNLLQLPQYFDLEIYTTGRLEKHLDALLRQIRNI
VEKHTDTDVLEACSKTYHALCNEEFTIFNRVDISRSQLIDELADKFNRLLEDFLQEGEEP
DEDDAYQVLSTLKRITAFHNAHDLSKWDLFACNYKLLKTGIENGDMPEQIVIHALQCTHY
VILWQLAKITESSSTKEDLLRLKKQMRVFCQICQHYLTNVNTTVKEQAFTILCDILMIFS
HQIMSGGRDMLEPLVYTPDSSLQSELLSFILDHVFIEQDDDNNSADGQQEDEASKIEALH
KRRNLLAAFCKLIVYTVVEMNTAADIFKQYMKYYNDYGDIIKETMSKTRQIDKIQCAKTL
ILSLQQLFNEMIQENGYNFDRSSSTFSGIKELARRFALTFGLDQLKTREAIAMLHKDGIE
FAFKEPNPQGESHPPLNLAFLDILSEFSSKLLRQDKRTVYVYLEKFMTFQMSLRREDVWL
PLMSYRNSLLAGGDDDTMSVI

Sequence of entity 2 (B), FASTA

>9EP3_2 Double-strand-break repair protein rad21 homolog (chains B)
VDPVEPMPTMTDQTTLVPNEEEAFALEPIDITVKETKAKRKRKLIVDSVKELDSKTIRAQ
LSDYSDIVTTLDLAPPTKKLMMWKETGGVEKLFSLPAQPLWNNRLLKLFTRCLTPLVPED
LRKRRKGGEADNLDEFLKEF

Sequence of entity 3 (C), FASTA

>9EP3_3 Wings apart-like protein homolog (chains C)
KRSPTKAVYNARHWNHPDSEEL

Primary citation

Structural basis for cohesin release and control of genome looping by WAPL. Graham, J.J., Panne, D. To be published.

Other PDB entries of the same protein (UniProt Q8N3U4 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6QNX 2.7 Å, Structure of the SA2/SCC1/CTCF complex
4PJW 2.85 Å, crystal structure of human Stromal Antigen 2 (SA2) in complex with Sister Chromatid…
9HMV 2.9 Å, Cryo-EM structure of SA2-SCC1 complex at 2.9 angstrom
4PK7 2.95 Å, crystal structure of human Stromal Antigen 2 (SA2) in complex with Sister Chromatid…
4PJU 3.05 Å, crystal structure of human Stromal Antigen 2 (SA2) in complex with Sister Chromatid…
9HX9 3.07 Å, Structure of the SA2/SCC1/MCM3 complex
7ZJS 3.24 Å, Structural basis of centromeric cohesion protection by SGO1
9HMS 3.4 Å, Cryo-EM structure of human separase bound to SCC1 (310-550 aa) and SA2
8K4D 3.52 Å, Structure of the SA2/Scc1/CENP_U complex

Browse structure collections

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