9SQY: ARISC(E33A)-RAP80:K63-Ub7 complex

Cryo-EM structure of the ARISC(E33A)-RAP80:K63-Ub7 complex (Composite map). Determined by electron microscopy at 2.92 Å resolution. Released 5 Aug 2026.

Method: Electron microscopy
Resolution: 2.92 Å
Organism: Homo sapiens
Chains: 16
Atoms: 23,659
Mol. weight: 546.08 kDa
Ligands: ZN
Released: 5 Aug 2026

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

Secondary structure: helices and β-sheets

9SQY contains 104 α-helices and 151 β-strands across 16 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: 10 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	11-15	5	34
α-helix	16-26	11
β-strand	35-42	8	34
β-strand	71-79	9	34
β-strand	84-85	2	25
β-strand	90-92	3	25
α-helix	94-98	5
α-helix	100-111	12
β-strand	116-123	8	34
α-helix	133-142	10
β-strand	150-160	11	34
β-strand	165-177	13	34
α-helix	178-179	2
β-strand	209-213	5	34
β-strand	216-219	4	34
α-helix	224-225	2
α-helix	226-251	26
α-helix	258-275	18
α-helix	276-280	5
α-helix	281-315	35

Chain B: 8 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	11-15	5	1
α-helix	16-26	11
β-strand	35-42	8	1
β-strand	71-79	9	1
α-helix	94-111	18
β-strand	116-125	10	1
α-helix	133-145	13
β-strand	150-160	11	1
β-strand	165-174	10	1
β-strand	212-214	3	1
β-strand	216-219	4	1
α-helix	227-232	6
α-helix	234-252	19
α-helix	258-275	18
α-helix	276-280	5
α-helix	281-314	34

Chain C: 7 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	7-11	5	34
α-helix	12-23	12
β-strand	29-39	11	34
β-strand	57-67	11	34
β-strand	74	1	35
β-strand	80	1	35
α-helix	82-88	7
β-strand	95-102	8	34
α-helix	112-125	14
β-strand	131-139	9	34
β-strand	146-154	9	34
β-strand	163	1	34
β-strand	166-169	4	34
α-helix	171-173	3
α-helix	189-197	9
β-strand	203	1	36
β-strand	209	1	36
α-helix	210-256	47
α-helix	278-287	10
β-strand	298-300	3	20

Chain D: 9 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	4-11	8	1
α-helix	12-23	12
β-strand	29-44	16	1
β-strand	52-67	16	1
β-strand	74	1	2
β-strand	80	1	2
α-helix	82-88	7
β-strand	95-102	8	1
α-helix	112-125	14
β-strand	131-139	9	1
β-strand	146-154	9	1
β-strand	163	1	1
β-strand	166-169	4	1
α-helix	171-173	3
α-helix	189-197	9
α-helix	199-202	4
β-strand	203	1	3
β-strand	209	1	3
α-helix	210-255	46
α-helix	278-286	9
α-helix	289-294	6
β-strand	298-300	3	4
β-strand	306	1	4

Chain E: 16 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	3-7	5
β-strand	10	1	5
α-helix	15-24	10
β-strand	36-41	6	6
β-strand	53	1	5
β-strand	55-62	8	6
β-strand	65-72	8	6
α-helix	81-82	2
β-strand	83-85	3	6
α-helix	96-98	3
α-helix	100-103	4
α-helix	112-131	20
α-helix	139-147	9
α-helix	149-152	4
β-strand	172-176	5	7
α-helix	184-186	3
β-strand	194	1	8
β-strand	201-207	7	7
β-strand	215-221	7	7
α-helix	223-228	6
α-helix	237-240	4
α-helix	249-281	33
β-strand	288-289	2	9
β-strand	296-303	8	9
β-strand	306-313	8	9
α-helix	318-320	3
α-helix	322-323	2
β-strand	324-328	5	9
β-strand	341-342	2	9
α-helix	355-369	15
α-helix	371-379	9

Chain F: 13 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	3-7	5
α-helix	15-24	10
β-strand	36-37	2	10
β-strand	41	1	10
β-strand	55-62	8	10
β-strand	65-72	8	10
β-strand	83-85	3	10
α-helix	100-103	4
α-helix	112-131	20
α-helix	132-134	3
α-helix	139-146	8
α-helix	149-152	4
β-strand	155-158	4	11
β-strand	163	1	12
α-helix	165-167	3
β-strand	168	1	12
β-strand	171-176	6	11
β-strand	201-207	7	11
β-strand	215	1	11
β-strand	218-221	4	11
α-helix	223-228	6
α-helix	246-281	36
β-strand	286-289	4	13
β-strand	296-301	6	13
β-strand	308-313	6	13
α-helix	322-323	2
β-strand	324-328	5	13
β-strand	341-344	4	13
α-helix	355-366	12
α-helix	371-379	9

Chain G: 8 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	93	1	14
β-strand	94-100	7	15
α-helix	103-105	3
β-strand	111	1	16
β-strand	112	1	17
β-strand	116	1	17
α-helix	120-138	19
β-strand	143-149	7	15
β-strand	154-155	2	15
β-strand	160	1	15
α-helix	164-171	8
α-helix	183-191	9
α-helix	206-207	2
β-strand	210	1	14
β-strand	211-213	3	15
β-strand	216-217	2	15
α-helix	230-234	5
β-strand	241-243	3	15
β-strand	245-249	5	15
α-helix	262-267	6
β-strand	279-283	5	15
β-strand	287	1	16
α-helix	289-297	9

Chain H: 10 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	81-84	4	4
β-strand	93-100	8	18
α-helix	104-106	3
β-strand	111	1	19
β-strand	117	1	19
α-helix	120-138	19
β-strand	143-149	7	18
β-strand	153-155	3	18
β-strand	160	1	18
α-helix	163-170	8
α-helix	183-192	10
α-helix	206-207	2
β-strand	210-217	8	18
α-helix	220-221	2
α-helix	230-237	8
β-strand	241-249	9	18
α-helix	253-254	2
α-helix	265-270	6
β-strand	279-283	5	18
β-strand	287	1	19
α-helix	289-297	9

8 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
BRCA1-A complex subunit Abraxas 1	C, D	protein	446	Homo sapiens	Q6UWZ7 (AlphaFold model)
BRISC and BRCA1-A complex member 2	E, F	protein	385	Homo sapiens	Q9NXR7 (AlphaFold model)
BRISC and BRCA1-A complex member 1	G, H	protein	329	Homo sapiens	Q9NWV8 (AlphaFold model)
BRCA1-A complex subunit RAP80	I, J	protein	724	Homo sapiens	Q96RL1 (AlphaFold model)
Ubiquitin	K, L, M, N, O, P	protein	76	Homo sapiens	P0CG48
Lys-63-specific deubiquitinase BRCC36	A, B	protein	316	Homo sapiens	P46736

Sequence of entity 1 (C, D), FASTA

>9SQY_1 BRCA1-A complex subunit Abraxas 1 (chains C, D)
MWSHPQFEKGGGSGGGSGGSAWSHPQFEKLEVLFQGTMEGESTSAVLSGFVLGALAFQHL
NTDSDTEGFLLGEVKGEAKNSITDSQMDDVEVVYTIDIQKYIPCYQLFSFYNSSGEVNEQ
ALKKILSNVKKNVVGWYKFRRHSDQIMTFRERLLHKNLQEHFSNQDLVFLLLTPSIITES
CSTHRLEHSLYKPQKGLFHRVPLVVANLGMSEQLGYKTVSGSCMSTGFSRAVQTHSSKFF
EEDGSLKEVHKINEMYASLQEELKSICKKVEDSEQAVDKLVKDVNRLKREIEKRRGAQIQ
AAREKNIQKDPQENIFLCQALRTFFPNSEFLHSCVMSLKNRHVSKSSCNYNHHLDVVDNL
TLMVEHTDIPEASPASTPQIIKHKALDLDDRWQFKRSRLLDTQDKRSKADTGSSNQDKAS
KMSSPETDEEIEKMKGFGEYSRSPTF

Sequence of entity 2 (E, F), FASTA

>9SQY_2 BRISC and BRCA1-A complex member 2 (chains E, F)
GAMSPEVALNRISPMLSPFISSVVRNGKVGLDATNCLRITDLKSGCTSLTPGPNCDRFKL
HIPYAGETLKWDIIFNAQYPELPPDFIFGEDAEFLPDPSALQNLASWNPSNPECLLLVVK
ELVQQYHQFQCSRLRESSRLMFEYQTLLEEPQYGENMEIYAGKKNNWTGEFSARFLLKLP
VDFSNIPTYLLKDVNEDPGEDVALLSVSFEDTEATQVYPKLYLSPRIEHALGGSSALHIP
AFPGGGCLIDYVPQVCHLLTNKVQYVIQGYHKRREYIAAFLSHFGTGVVEYDAEGFTKLT
LLLMWKDFCFLVHIDLPLFFPRDQPTLTFQSVYHFTNSGQLYSQAQKNYPYSPRWDGNEM
AKRAKAYFKTFVPQFQEAAFANGKL

Sequence of entity 3 (G, H), FASTA

>9SQY_3 BRISC and BRCA1-A complex member 1 (chains G, H)
MEVAEPSSPTEEEEEEEEHSAEPRPRTRSNPEGAEDRAVGAQASVGSRSEGEGEAASADD
GSLNTSGAGPKSWQVPPPAPEVQIRTPRVNCPEKVIICLDLSEEMSLPKLESFNGSKTNA
LNVSQKMIEMFVRTKHKIDKSHEFALVVVNDDTAWLSGLTSDPRELCSCLYDLETASCST
FNLEGLFSLIQQKTELPVTENVQTIPPPYVVRTILVYSRPPCQPQFSLTEPMKKMFQCPY
FFFDVVYIHNGTEEKEEEMSWKDMFAFMGSLDTKGTSYKYEVALAGPALELHNCMAKLLA
HPLQRPCQSHASYSLLEEEDEAIEVEATV

Sequence of entity 4 (I, J), FASTA

>9SQY_4 BRCA1-A complex subunit RAP80 (chains I, J)
GAMGSMPRRKKKVKEVSESRNLEKKDVETTSSVSVKRKRRLEDAFIVISDSDGEEPKEEN
GLQKTKTKQSNRAKCLAKRKIAQMTEEEQFALALKMSEQEAREVNSQEEEEEELLRKAIA
ESLNSCRPSDASATRSRPLATGPSSQSHQEKTTDSGLTEGIWQLVPPSLFKGSHISQGNE
AEEREEPWDHTEKTEEEPVSGSSGSWDQSSQPVFENVNVKSFDRCTGHSAEHTQCGKPQE
STGRGSAFLKAVQGSGDTSRHCLPTLADAKGLQDTGGTVNYFWGIPFCPDGVDPNQYTKV
ILCQLEVYQKSLKMAQRQLLNKKGFGEPVLPRPPSLIQNECGQGEQASEKNECISEDMGD
EDKEERQESRASDWHSKTKDFQESSIKSLKEKLLLEEEPTTSHGQSSQGIVEETSEEGNS
VPASQSVAALTSKRSLVLMPESSAEEITVCPETQLSSSETFDLEREVSPGSRDILDGVRI
IMADKEVGNKEDAEKEVAISTFSSSNQVSCPLCDQCFPPTKIERHAMYCNGLMEEDTVLT
RRQKEAKTKSDSGTAAQTSLDIDKNEKCYLCKSLVPFREYQCHVDSCLQLAKADQGDGPE
GSGRACSTVEGKWQQRLKNPKEKGHSEGRLLSFLEQSEHKTSDADIKSSETGAFRVPSPG
MEEAGCSREMQSSFTRRDLNESPVKSFVSISEATDCLVDFKKQVTVQPGSRTRTKAGRGR
RRKF

Sequence of entity 5 (K, L, M, N, O, P), FASTA

>9SQY_5 Ubiquitin (chains K, L, M, N, O, P)
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN
IQKESTLHLVLRLRGG

Sequence of entity 6 (A, B), FASTA

>9SQY_6 Lys-63-specific deubiquitinase BRCC36 (chains A, B)
MAVQVVQAVQAVHLESDAFLVCLNHALSTEKEAVMGLCIGELNDDTRSDSKFAYTGTEMR
TVAEKVDAVRIVHIHSVIILRRSDKRKDRVEISPEQLSAASTEAERLAELTGRPMRVVGW
YHSHPHITVWPSHVDVRTQAMYQMMDQGFVGLIFSCFIEDKNTKTGRVLYTCFQSIQAQK
SSESLHGPRDFWSSSQHISIEGQKEEERYERIEIPIHIVPHVTIGKVCLESAVELPKILC
QEEQDAYRRIHSLTHLDSVTKIHNGSVFTKNLCSQMSAVSGPLLQWLEDRLEQNQQHLQE
LQQEKEELMQELSSLE

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	2

Primary citation

Mechanism of K63-linked polyubiquitin recognition and cleavage by the BRCA1-A complex. Foglizzo, M., Datta, A., Degtjarik, O. et al. Nat Commun (2026) 17. DOI 10.1038/s41467-026-75795-y · PubMed

Other PDB entries of the same protein (UniProt Q6UWZ7 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4Y2G 2.5 Å, Structure of BRCA1 BRCT domains in complex with Abraxas single phosphorylated peptide
9SMP 3.0 Å, BRCA1-A complex bound to K63-polyUbATA - open form double State P
9SMN 3.2 Å, BRCA1-A complex bound to K63-polyUbATA - open form StateC StateP
9SNA 3.2 Å, BRCA1-A complex bound to K63-diUbATA - open form StateC StateP
9SQW 3.2 Å, Cryo-EM structure of the ARISCdC(E33A):K63-Ub7 complex (Composite map)
9SQV 3.21 Å, Cryo-EM structure of the ARISCdC(E33A):K63-Ub4 complex (Composite map)
9SMR 3.25 Å, Structure of apo BRCA1-A complex in presence of K63-oligoUbATA
9SMS 3.3 Å, BRCA1-A complex: Ubiquitin bound to BRE at the wrist site (focused 3D class)
9SO9 3.4 Å, BRCA1-A complex bound to K63-oligoUbATA - closed form StateC*
4JLU 3.5 Å, Crystal structure of BRCA1 BRCT with doubly phosphorylated Abraxas
4Y18 3.5 Å, Structure of BRCA1 BRCT domains in complex with Abraxas double phosphorylated peptide
4U4A 3.51 Å, Complex Structure of BRCA1 BRCT with singly phospho Abraxas

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